@Comment { \documentclass{article} \usepackage{url} \begin{document} This Test originally published in \cite{OpenKIM-TE:406365327721:000a, OpenKIM-TE:406365327721:000b} is archived in \cite{OpenKIM-TE:406365327721:000, OpenKIM-TD:495406822220:000, tadmor:elliott:2011, elliott:tadmor:2011}. \bibliographystyle{vancouver} \bibliography{kimcite-TE_406365327721_000.bib} \end{document} } @Misc{OpenKIM-TE:406365327721:000, author = {I Nikiforov and Ellad B. Tadmor and Daniel S. Karls and Moon-ki Choi}, title = {{U}nconstrained equilibrium crystal structure and energy of {G}raphite expressed in {CHARMM}-{GUI} {INTERFACE} atom types and bonding v000}, howpublished = {OpenKIM, \url{https://openkim.org/cite/TE_406365327721_000}}, keywords = {OpenKIM, Test, TE_406365327721_000}, publisher = {OpenKIM}, year = 2023, } @Misc{OpenKIM-TD:495406822220:000, author = {I Nikiforov and Ellad B. Tadmor and Moon-ki Choi and Daniel S. Karls}, title = {{E}quilibrium structure and energy for a crystal specified using {LAMMPS} type labels at zero temperature and pressure v000}, doi = {10.25950/86dce899}, howpublished = {OpenKIM, \url{https://doi.org/10.25950/86dce899}}, keywords = {OpenKIM, Test Driver, TD_495406822220_000}, publisher = {OpenKIM}, year = 2023, } @Article{tadmor:elliott:2011, author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker}, title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels}, journal = {{JOM}}, year = {2011}, volume = {63}, number = {7}, pages = {17}, doi = {10.1007/s11837-011-0102-6}, } @Misc{elliott:tadmor:2011, author = {Ryan S. Elliott and Ellad B. Tadmor}, title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})}, howpublished = {\url{https://openkim.org/kim-api}}, publisher = {OpenKIM}, year = 2011, doi = {10.25950/ff8f563a}, } @Article{OpenKIM-TE:406365327721:000a, 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. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008}, author = {Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil}, doi = {https://doi.org/10.1002/jcc.20945}, eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945}, journal = {Journal of Computational Chemistry}, keywords = {molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace}, number = {11}, pages = {1859-1865}, title = {CHARMM-GUI: A web-based graphical user interface for CHARMM}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945}, volume = {29}, year = {2008}, } @Article{OpenKIM-TE:406365327721:000b, 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}, doi = {10.1021/acs.jctc.1c00996}, eprint = { https://doi.org/10.1021/acs.jctc.1c00996 }, journal = {Journal of Chemical Theory and Computation}, note = {PMID: 34871001}, number = {1}, pages = {479-493}, title = {CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems}, url = {https://doi.org/10.1021/acs.jctc.1c00996}, volume = {18}, year = {2022}, }