{"species": ["Fe"], "material": "Iron", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "484833569828", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Iron/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IFE"} {"species": ["Al", "H", "O", "Si"], "material": "Montmorillonite", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "912341279351", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Montmorillonite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IHOY IOY1 IOY2 IOY3 IOY4 IOY5 IOY6 IOY7 IOY8 IOY9 IAY1 IAY2 ISY1 ISY2"} {"species": ["Al", "O"], "material": "Aluminum-Oxide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "949159786812", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Aluminum-Oxide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "OAL1 ALO1"} {"species": ["Cr", "O"], "material": "Chromium-Oxide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "396348672999", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Chromium-Oxide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "OCR1 CRO1"} {"species": ["Pt"], "material": "Platinum", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "302533303643", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Platinum/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IPT"} {"species": ["Yb"], "material": "Ytterbium", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "098654223594", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Ytterbium/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IYB"} {"species": ["Au"], "material": "Gold", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "567848581181", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Gold/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IAU"} {"species": ["Ca", "O"], "material": "Calcium-Oxide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "816860586933", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Calcium-Oxide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "OCA1 CAO1"} {"species": ["Ce"], "material": "Cerium", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "192291552296", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Cerium/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "ICE"} {"species": ["Ca", "H", "O", "S"], "material": "Hemihydrate", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "408150552107", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Hemihydrate/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IH_SC IOCS IO_SC ISCS ICA_G"} {"species": ["Rh"], "material": "Rhodium", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "781546079162", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Rhodium/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IRH"} {"species": ["Ir"], "material": "Iridium", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "185896031186", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Iridium/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IIR"} {"species": ["O", "Si"], "material": "Alpha-Cristobalite", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "610986400767", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Alpha-Cristobalite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IOC23 ISC4"} {"species": ["Al", "H", "O", "Si"], "material": "Kaolinite", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "770977003873", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Kaolinite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IHOK IHOY IOY1 IOY2 IOY3 IOY4 IOY5 IOY6 IOY7 IOY8 IOY9 IAY1 IAY2 ISY1 ISY2"} {"species": ["Fe", "O"], "material": "Iron-Oxide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "213961911992", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Iron-Oxide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "OFE1 FEO1"} {"species": ["Ca", "O", "Si"], "material": "Tricalcium-Silicate", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "356659368071", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Tricalcium-Silicate/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IOC1 IOC2 ISC1 ICA_S"} {"species": ["Al", "H", "O", "Si"], "material": "Pyrophyllite", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "850892375316", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Pyrophyllite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IHOY IOY1 IOY2 IOY3 IOY4 IOY5 IOY6 IOY7 IOY8 IOY9 IAY1 IAY2 ISY1 ISY2"} {"species": ["Ca", "H", "O"], "material": "Calcium-Hydroxide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "290999115954", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Calcium-Hydroxide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IHOP OCA2 CAO2"} {"species": ["Pd"], "material": "Palladium", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "349496708972", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Palladium/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IPD"} {"species": ["H", "Mg", "O"], "material": "Magnesium-Hydroxide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "760940522921", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Magnesium-Hydroxide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IHOP OMG2 MGO2"} {"species": ["Ac"], "material": "Actinium", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "597964364715", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Actinium/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IAC"} {"species": ["Pb"], "material": "Lead", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "197677336795", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Lead/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IPB"} {"species": ["H", "Ni", "O"], "material": "Nickel-Hydroxide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "190023696711", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Nickel-Hydroxide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IHOP ONI2 NIO2"} {"species": ["Es"], "material": "Einsteinium", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "477588950321", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Einsteinium/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IES"} {"species": ["C"], "material": "Graphite", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "406365327721", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Graphite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "ICGE ICG1"} {"species": ["Ca"], "material": "Calcium", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "155275770946", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Calcium/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "ICA"} {"species": ["Mg", "O"], "material": "Magnesium-Oxide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "400345532746", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Magnesium-Oxide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "OMG1 MGO1"} {"species": ["Ni"], "material": "Nickel", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "966841164937", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Nickel/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "INI"} {"species": ["Ca", "H", "O", "Si"], "material": "Tobemorite", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "046183663521", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Tobemorite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IHOY IH_SC IOC12 IOC13 IOC14 IO_SC ISC2 ISC3 ICA_T"} {"species": ["Ni", "O"], "material": "Nickel-Oxide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "784462135228", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Nickel-Oxide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "ONI1 NIO1"} {"species": ["Mo", "S"], "material": "Molybdenum-Disulfide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "872188620196", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Molybdenum-Disulfide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "ISM1 ISM2 ISM3 ISM4 IMO1 IMO2"} {"species": ["O", "Si"], "material": "Alpha-Quartz", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "723122523764", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Alpha-Quartz/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IOC23 ISC4"} {"species": ["Cu"], "material": "Copper", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "223045501550", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Copper/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "ICU"} {"species": ["Al", "Ca", "O"], "material": "Tricalcium-Aluminate", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "889636295875", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Tricalcium-Aluminate/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IOC3 IOC4 IAC1 ICA_A"} {"species": ["Al", "H", "K", "O", "Si"], "material": "Muscovite", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "755120994678", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Muscovite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IHOY IOY1 IOY2 IOY3 IOY4 IOY5 IOY6 IOY7 IOY8 IOY9 IAY1 IAY2 IAYT2 ISY1 ISY2 IK_CM"} {"species": ["S", "W"], "material": "Tungsten-Disulfide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "507357313954", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Tungsten-Disulfide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "ISW1 ISW2 ISW3 ISW4 IW1 IW2"} {"species": ["Sr"], "material": "Strontium", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "353530475638", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Strontium/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "ISR"} {"species": ["Ca", "H", "O", "S"], "material": "Gypsum", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "786449451894", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Gypsum/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IH_SC IOCS IO_SC ISCS ICA_G"} {"species": ["Ca", "O", "S"], "material": "Anhydrite", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "889550055760", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Anhydrite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IOCS ISCS ICA_G"} {"species": ["Co", "Li", "O"], "material": "Lithium-Cobalt-Oxide", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "278739671768", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Lithium-Cobalt-Oxide/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "LI OCO1 OCO2 COO"} {"species": ["Al"], "material": "Aluminum", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "127974406309", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Aluminum/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IAL"} {"species": ["Ag"], "material": "Silver", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "967841411038", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Silver/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "IAG"} {"species": ["Th"], "material": "Thorium", "modeltype": "CHARMM-GUI INTERFACE", "matching_models": "[\"charmm-gui/\"]", "version": "000", "kimnum": "407162758668", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/charmm-gui/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/CHARMM-GUI/Thorium/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "ITH"} {"species": ["Ca", "F"], "prototype_label": "AB2_cF12_225_a_c", "material": "AB2_cF12_225_a_c:Ca:F", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "185882332954", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB2_cF12_225_a_c_Ca_F/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/FCC/Ca1F2_ICSD_44937/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "CaC CaS FC FS"} {"species": ["Ca", "F"], "prototype_label": "AB2_hR3_166_a_c", "material": "AB2_hR3_166_a_c:Ca:F", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "602903071008", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB2_hR3_166_a_c_Ca_F/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/RHL/Ca2F4_ICSD_246961/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "CaC CaS FC FS"} {"species": ["Ca", "F"], "prototype_label": "AB2_oP12_62_c_2c", "material": "AB2_oP12_62_c_2c:Ca:F", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "372718531987", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB2_oP12_62_c_2c_Ca_F/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/ORC/Ca1F2_ICSD_656449/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "CaC CaS FC FS"} {"species": ["Ca", "F"], "prototype_label": "AB2_oP6_26_a_ab", "material": "AB2_oP6_26_a_ab:Ca:F", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "090943626130", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB2_oP6_26_a_ab_Ca_F/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/ORC/Ca1F2_ICSD_51239/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "CaC CaS FC FS"} {"species": ["Ca", "F"], "prototype_label": "AB2_tP3_123_a_e", "material": "AB2_tP3_123_a_e:Ca:F", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "626869503943", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB2_tP3_123_a_e_Ca_F/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/TET/Ca1F2_ICSD_51237/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "CaC CaS FC FS"} {"species": ["Cl", "Na"], "prototype_label": "AB_cF8_225_a_b", "material": "AB_cF8_225_a_b:Cl:Na", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "102563389665", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_cF8_225_a_b_Cl_Na/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/FCC/Cl1Na1_ICSD_60280/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "ClC ClS NaC NaS"} {"species": ["Cl", "Na"], "prototype_label": "AB_cP2_221_a_b", "material": "AB_cP2_221_a_b:Cl:Na", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "887131284947", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_cP2_221_a_b_Cl_Na/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/CUB/Cl1Na1_ICSD_622368/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "ClC ClS NaC NaS"} {"species": ["Mg", "O"], "prototype_label": "AB_cF8_225_a_b", "material": "AB_cF8_225_a_b:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "816421242166", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_cF8_225_a_b_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/FCC/Mg1O1_ICSD_159375/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB_cP12_223_c_d", "material": "AB_cP12_223_c_d:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "312580027644", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_cP12_223_c_d_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/CUB/Mg1O1_ICSD_181465/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB_hP2_187_a_d", "material": "AB_hP2_187_a_d:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "069188318101", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_hP2_187_a_d_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/HEX/Mg1O1_ICSD_166273/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB_hP24_192_l_l", "material": "AB_hP24_192_l_l:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "340085167281", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_hP24_192_l_l_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/HEX/Mg1O1_ICSD_181463/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB_hP24_194_ab2f_e2f", "material": "AB_hP24_194_ab2f_e2f:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "434184180552", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_hP24_194_ab2f_e2f_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/HEX/Mg1O1_ICSD_181457/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB_hP4_186_b_b", "material": "AB_hP4_186_b_b:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "647349572898", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_hP4_186_b_b_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/HEX/Mg1O1_ICSD_181461/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB_hP4_194_c_d", "material": "AB_hP4_194_c_d:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "140848426356", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_hP4_194_c_d_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/HEX/Mg1O1_ICSD_162607/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB_hR16_166_ab3c_4c", "material": "AB_hR16_166_ab3c_4c:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "050458331662", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_hR16_166_ab3c_4c_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/RHL/Mg1O1_ICSD_181459/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB_mC48_8_12a_12a", "material": "AB_mC48_8_12a_12a:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "631244022605", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_mC48_8_12a_12a_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/MCLC/Mg1O1_ICSD_181464/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB_mC48_15_3f_3f", "material": "AB_mC48_15_3f_3f:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "602605063148", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_mC48_15_3f_3f_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/MCLC/Mg1O1_ICSD_181466/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB_oI32_72_2j_2j", "material": "AB_oI32_72_2j_2j:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "486018722972", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_oI32_72_2j_2j_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/ORCI/Mg1O1_ICSD_181462/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB_oI48_72_3j_3j", "material": "AB_oI48_72_3j_3j:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "006933107939", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB_oI48_72_3j_3j_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/ORCI/Mg1O1_ICSD_181460/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Mg", "O"], "prototype_label": "AB2_cP12_205_a_c", "material": "AB2_cP12_205_a_c:Mg:O", "modeltype": "core-shell", "matching_models": "[\"born/coul/long/cs\"]", "version": "000", "kimnum": "068755949348", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/cs/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/coreshell/AB2_cP12_205_a_c_Mg_O/input0.dat"], "comment": "Initial geometry obtained from the following URL(s): http://aflowlib.duke.edu/AFLOWDATA/ICSD_WEB/CUB/Mg1O2_ICSD_35479/CONTCAR.relax.vasp", "source_citations": [" \"title\" \"AFLOWLIB.ORG: A distributed materials properties repository from high-throughput ab initio calculations\"\n \"journal\" \"Computational Materials Science\"\n \"volume\" \"58\"\n \"pages\" \"227-235\"\n \"year\" \"2012\"\n \"issn\" \"0927-0256\"\n \"doi\" \"https://doi.org/10.1016/j.commatsci.2012.02.002\"\n \"url\" \"https://www.sciencedirect.com/science/article/pii/S0927025612000687\"\n \"author\" \"Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy\"\n \"keywords\" \"High-throughput, Combinatorial materials science, Ab initio, AFLOW, Materials genome initiative\"\n \"abstract\" \"Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.\"\n \"recordtype\" \"article\""], "atom_type_labels": "Mg OC OS"} {"species": ["Al", "H", "O", "Si"], "material": "Montmorillonite", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "317102643046", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Montmorillonite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "hoy oy1 oy2 oy3 oy4 oy5 oy6 oy7 oy8 oy9 ay1 ay2 sy1 sy2"} {"species": ["Pt"], "material": "Platinum", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "827537199504", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Platinum/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "Pt"} {"species": ["Au"], "material": "Gold", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "018048185561", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Gold/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "Au"} {"species": ["O", "Si"], "material": "Alpha-Cristobalite", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "956746767764", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Alpha-Cristobalite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "oc23 sc4"} {"species": ["Al", "H", "O", "Si"], "material": "Kaolinite", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "313060772354", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Kaolinite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "hok hoy oy1 oy2 oy3 oy4 oy5 oy6 oy7 oy8 oy9 ay1 ay2 sy1 sy2"} {"species": ["Ca", "O", "Si"], "material": "Tricalcium-Silicate", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "036658485235", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Tricalcium-Silicate/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "oc1 oc2 sc1 ca++"} {"species": ["Al", "H", "O", "Si"], "material": "Pyrophyllite", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "060007452167", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Pyrophyllite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "hoy oy1 oy2 oy3 oy4 oy5 oy6 oy7 oy8 oy9 ay1 ay2 sy1 sy2"} {"species": ["Pd"], "material": "Palladium", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "743067765159", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Palladium/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "Pd"} {"species": ["Pb"], "material": "Lead", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "935633991872", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Lead/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "Pb"} {"species": ["Ni"], "material": "Nickel", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "780511124020", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Nickel/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "Ni"} {"species": ["Ca", "H", "O", "Si"], "material": "Tobemorite", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "068767742876", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Tobemorite/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "hoy h* oc12 oc13 oc14 o* sc2 sc3 ca+t"} {"species": ["O", "Si"], "material": "Alpha-Quartz", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "494593576827", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Alpha-Quartz/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "oc23 sc4"} {"species": ["Cu"], "material": "Copper", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "217597096512", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Copper/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "Cu"} {"species": ["Al", "Ca", "O"], "material": "Tricalcium-Aluminate", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "386531012571", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Tricalcium-Aluminate/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "oc3 oc4 ac1 ca+a"} {"species": ["Al"], "material": "Aluminum", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "741008777397", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Aluminum/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "Al"} {"species": ["Ag"], "material": "Silver", "modeltype": "PCFF-INTERFACE", "matching_models": "[\"class2\"]", "version": "000", "kimnum": "314538851176", "kim_user_id": "4ad03136-ed7f-4316-b586-1e94ccceb311", "FILES_TO_COPY": ["/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/symfiles/pcff/sym.txt", "/home/openkim/test-drivers/EquilibriumCrystalStructure_Unconstrained_TypeLabels__TD_495406822220_000/bonded_util/../Tests/PCFF-IFF/Silver/input0.dat"], "comment": "Initial geometry and bonding topology obtained from CHARMM-GUI.", "source_citations": [" \"abstract\" \"CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2008\"\n \"author\" \"Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil\"\n \"doi\" \"https://doi.org/10.1002/jcc.20945\"\n \"eprint\" \"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945\"\n \"journal\" \"Journal of Computational Chemistry\"\n \"keywords\" \"molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace\"\n \"number\" \"11\"\n \"pages\" \"1859-1865\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI: A web-based graphical user interface for CHARMM\"\n \"url\" \"https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945\"\n \"volume\" \"29\"\n \"year\" \"2008\"", " \"author\" \"Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil\"\n \"doi\" \"10.1021/acs.jctc.1c00996\"\n \"eprint\" \" https://doi.org/10.1021/acs.jctc.1c00996 \"\n \"journal\" \"Journal of Chemical Theory and Computation\"\n \"note\" \"PMID: 34871001\"\n \"number\" \"1\"\n \"pages\" \"479-493\"\n \"recordtype\" \"article\"\n \"title\" \"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems\"\n \"url\" \"https://doi.org/10.1021/acs.jctc.1c00996\"\n \"volume\" \"18\"\n \"year\" \"2022\""], "atom_type_labels": "Ag"}