| Title
A single sentence description.
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Interface Force Field (IFF) parameters due to Heinz et al. as used in the CHARMM-GUI input generator v000 |
|---|---|
| Description | This is the subset of the Interface Force Field (IFF) implemented in CHARMM-GUI as of 2023-2-23. It contains parameters for gas molecules, FCC metals, metal oxides, metal hydroxides, battery oxides, clay minerals, mica, calcium sulfates, cement minerals, tobermorite, silica, hydroxyapatite, transition-metal dichalcogenides, and graphitic materials. IFF atom type labels are proprietary to the CHARMM-GUI implementation, equal to IFF force field types starting with an added letter “I”. This implementation of IFF covers only parameters in CHARMM using a 12-6 LJ potential. It excludes a separate set of IFF parameters compatible with CFF, PCFF, and COMPASS using a 9-6 LJ potential, as well as customized parameters for OPLS-AA and AMBER for selected compounds. This implementation also excludes IFF parameters for polymers (PEG, PMMA), and several solvents. The parameters archived in this OpenKIM model for Molybdenum Disulfide are tuned for a more accurate equilibrium crystal structure, and differ slightly from those in CHARMM-GUI which are tuned for more accurate infrared spectra. See complete documentation and updates on the website (https://bionanostructures.com/interface-md/). |
| Species
The supported atomic species.
| Ac, Ag, Al, Au, C, Ca, Ce, Co, Cr, Cu, Es, Fe, H, Ir, K, Li, Mg, Mo, Ni, O, P, Pb, Pd, Pt, Rh, S, Si, Sr, Th, W, Yb |
| Disclaimer
A statement of applicability provided by the contributor, informing users of the intended use of this KIM Item.
|
Partial charges are not provided with this Simulator Model. The user must assign their own charges when creating atoms. CHARMM .rtf files for this model can be found on the IFF website, or packaged with any structure obtained from CHARMM-GUI. A converter for CHARMM-GUI is available. |
| Content Origin | charmm-gui.org |
| Contributor |
I Nikiforov |
| Maintainer |
I Nikiforov |
| Developer |
Hendrik Heinz Fateme S. Emami Tzu-Jen Lin Ratan K. Mishra Juan Liu Chandrani Pramanik Krishan Kanhaiya Shiyi Wang |
| Published on KIM | 2023 |
| How to Cite |
This Simulator Model originally published in [1-7] is archived in OpenKIM [8-10]. [1] Heinz H, Vaia RA, Farmer BL, Naik RR. Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12-6 and 9-6 Lennard-Jones Potentials. The Journal of Physical Chemistry C [Internet]. 2008;112(44):17281–90. Available from: https://doi.org/10.1021/jp801931d doi:10.1021/jp801931d [2] Heinz H, Lin T-J, Kishore Mishra R, Emami FS. Thermodynamically Consistent Force Fields for the Assembly of Inorganic, Organic, and Biological Nanostructures: The INTERFACE Force Field. Langmuir [Internet]. 2013;29(6):1754–65. Available from: https://doi.org/10.1021/la3038846 doi:10.1021/la3038846 — (Primary Source) A primary source is a reference directly related to the item documenting its development, as opposed to other sources that are provided as background information. [3] Emami FS, Puddu V, Berry RJ, Varshney V, Patwardhan SV, Perry CC, et al. Force Field and a Surface Model Database for Silica to Simulate Interfacial Properties in Atomic Resolution. Chemistry of Materials [Internet]. 2014;26(8):2647–58. Available from: https://doi.org/10.1021/cm500365c doi:10.1021/cm500365c [4] Lin T-J, Heinz H. Accurate Force Field Parameters and pH Resolved Surface Models for Hydroxyapatite to Understand Structure, Mechanics, Hydration, and Biological Interfaces. The Journal of Physical Chemistry C [Internet]. 2016;120(9):4975–92. Available from: https://doi.org/10.1021/acs.jpcc.5b12504 doi:10.1021/acs.jpcc.5b12504 [5] Mishra RK, Kanhaiya K, Winetrout JJ, Flatt RJ, Heinz H. Force field for calcium sulfate minerals to predict structural, hydration, and interfacial properties. Cement and Concrete Research [Internet]. 2021;139:106262. Available from: https://www.sciencedirect.com/science/article/pii/S0008884620308814 doi:10.1016/j.cemconres.2020.106262 [6] Liu J, Zeng J, Zhu C, Miao J, Huang Y, Heinz H. Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition. Chem Sci [Internet]. 2020;11(33):8708–22. Available from: http://dx.doi.org/10.1039/D0SC01443E doi:10.1039/D0SC01443E [7] Kanhaiya K, Nathanson M, Veld PJ in ’t, Zhu C, Nikiforov I, Tadmor EB, et al. Accurate Force Fields for Atomistic Simulations of Oxides, Hydroxides, and Organic Hybrid Materials up to the Micrometer Scale. Journal of chemical theory and computation. 2023;19(22):8293–322. [8] Heinz H, Emami FS, Lin T-J, Mishra RK, Liu J, Pramanik C, et al. Interface Force Field (IFF) parameters due to Heinz et al. as used in the CHARMM-GUI input generator v000. OpenKIM; 2023. doi:10.25950/544c334f [9] Tadmor EB, Elliott RS, Sethna JP, Miller RE, Becker CA. The potential of atomistic simulations and the Knowledgebase of Interatomic Models. JOM. 2011;63(7):17. doi:10.1007/s11837-011-0102-6 [10] Elliott RS, Tadmor EB. Knowledgebase of Interatomic Models (KIM) Application Programming Interface (API). OpenKIM; 2011. doi:10.25950/ff8f563a Click here to download the above citation in BibTeX format. |
| Funding | Not available |
| Short KIM ID
The unique KIM identifier code.
| SM_232384752957_000 |
| Extended KIM ID
The long form of the KIM ID including a human readable prefix (100 characters max), two underscores, and the Short KIM ID. Extended KIM IDs can only contain alpha-numeric characters (letters and digits) and underscores and must begin with a letter.
| Sim_LAMMPS_IFF_CHARMM_GUI_HeinzLinMishra_2023_Nanomaterials__SM_232384752957_000 |
| DOI |
10.25950/544c334f https://doi.org/10.25950/544c334f https://commons.datacite.org/doi.org/10.25950/544c334f |
| KIM Item Type | Simulator Model |
| KIM API Version | 2.3 |
| Simulator Name
The name of the simulator as defined in kimspec.edn.
| LAMMPS |
| Potential Type | charmm |
| Simulator Potential | charmm-gui/interface/12_cut-off |
| Run Compatibility | special-purpose-models |
| Atom Type Labels
The supported particle types, if different from their atomic species.
|
{"ALO1" "Al", "IH1O" "H", "ICA" "Ca", "OCA1" "O", "NIO1" "Ni", "IOC9" "O", "NIO2" "Ni", "IK_CM" "K", "OCO2" "O", "IOY6" "O", "IRH" "Rh", "ICU" "Cu", "IHOK" "H", "ICPEO" "C", "IOY2" "O", "IHPEO" "H", "IAYT1" "Al", "LI" "Li", "ICA_S" "Ca", "IPB" "Pb", "ICA_H" "Ca", "ISC2" "Si", "ICA_T" "Ca", "CAO2" "Ca", "IOC10" "O", "MGO1" "Mg", "ISC3" "Si", "ITH" "Th", "AUL" "Au", "IOY5" "O", "IOC14" "O", "IAC2" "Al", "ISM4" "S", "IES" "Es", "IS_AN" "S", "IOC12" "O", "IOC8" "O", "AUD" "Au", "OCO1" "O", "ISY2" "Si", "IOC5" "O", "OMG1" "O", "ISCS" "S", "IYB" "Yb", "IO_SC" "O", "IMY1" "Mg", "CRO1" "Cr", "CAO1" "Ca", "N2G" "N", "IO2_SC" "O", "IOC7" "O", "ICA_G" "Ca", "OAL1" "O", "O2G" "O", "IOC1" "O", "IOAP1" "O", "IMO2" "Mo", "OCR1" "O", "ONI2" "O", "COO" "Co", "IOC13" "O", "IOAP2" "O", "IW2" "W", "ISW2" "S", "IAY2" "Al", "FEO1" "Fe", "IOC23" "O", "IOC6" "O", "IPAP" "P", "IOY7" "O", "MGO2" "Mg", "ISW4" "S", "IMO1" "Mo", "ISC4" "Si", "IOY9" "O", "IOC4" "O", "IOC11" "O", "OCA2" "O", "ICA_A" "Ca", "IOY8" "O", "IAY1" "Al", "IAL" "Al", "ICE" "Ce", "IAYT2" "Al", "ISY1" "Si", "ISM2" "S", "IPD" "Pd", "IHOY" "H", "IAG" "Ag", "IFE" "Fe", "ICGE" "IGNORE", "IOC2" "O", "ICA_E" "Ca", "IOY1" "O", "ISR" "Sr", "IOY3" "O", "ST" "S", "OFE1" "O", "IOCS" "O", "IOC3" "O", "IIR" "Ir", "ISW1" "S", "IAC1" "Al", "IH_SC" "H", "ICG1" "C", "ISM1" "S", "INI" "Ni", "IPT" "Pt", "AUS" "Au", "IOC24" "O", "H2G" "H", "IAU" "Au", "IHOP" "H", "ONI1" "O", "IOY4" "O", "ISM3" "S", "ISW3" "S", "IOPEO" "O", "OMG2" "O", "IHOC" "H", "IAC" "Ac", "IW1" "W", "ISC1" "Si"} |
This bar chart plot shows the mono-atomic body-centered cubic (bcc) lattice constant predicted by the current model (shown in the unique color) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.
(No matching species)This graph shows the cohesive energy versus volume-per-atom for the current mode for four mono-atomic cubic phases (body-centered cubic (bcc), face-centered cubic (fcc), simple cubic (sc), and diamond). The curve with the lowest minimum is the ground state of the crystal if stable. (The crystal structure is enforced in these calculations, so the phase may not be stable.) Graphs are generated for each species supported by the model.
(No matching species)This bar chart plot shows the mono-atomic face-centered diamond lattice constant predicted by the current model (shown in the unique color) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.
(No matching species)This graph shows the dislocation core energy of a cubic crystal at zero temperature and pressure for a specific set of dislocation core cutoff radii. After obtaining the total energy of the system from conjugate gradient minimizations, non-singular, isotropic and anisotropic elasticity are applied to obtain the dislocation core energy for each of these supercells with different dipole distances. Graphs are generated for each species supported by the model.
(No matching species)This bar chart plot shows the mono-atomic face-centered cubic (fcc) elastic constants predicted by the current model (shown in blue) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.
(No matching species)This bar chart plot shows the mono-atomic face-centered cubic (fcc) lattice constant predicted by the current model (shown in red) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.
(No matching species)This bar chart plot shows the intrinsic and extrinsic stacking fault energies as well as the unstable stacking and unstable twinning energies for face-centered cubic (fcc) predicted by the current model (shown in blue) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.
(No matching species)This bar chart plot shows the mono-atomic face-centered cubic (fcc) relaxed surface energies predicted by the current model (shown in blue) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.
(No matching species)This bar chart plot shows the mono-atomic simple cubic (sc) lattice constant predicted by the current model (shown in the unique color) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.
(No matching species)Partial charges are not provided with this Simulator Model. The user must assign their own charges when creating atoms. CHARMM .rtf files for this model can be found on the IFF website, or packaged with any structure obtained from CHARMM-GUI. A converter for CHARMM-GUI is available.
| Sim_LAMMPS_IFF_CHARMM_GUI_HeinzLinMishra_2023_Nanomaterials__SM_232384752957_000.txz | Tar+XZ | Linux and OS X archive |
| Sim_LAMMPS_IFF_CHARMM_GUI_HeinzLinMishra_2023_Nanomaterials__SM_232384752957_000.zip | Zip | Windows archive |