Welcome to WebFF’s documentation!¶
WebFF¶
WebFF is an open and extensible molecular dynamics force-field (FF) repository, designed to support the Materials Genome Initiative (MGI) for organic and related soft materials. The repository is built using the NIST Materials Data Curation System (MDCS) [link] which supports ontology based database descriptions using XML schema.
Features¶
Here are some of the main features of WebFF:
- Users interact with the repository through two main portals. The Data Exploration Portal [link] supports search for force-field data based on the curated metadata descriptors and download in a number for common formats. We will work with the user community to expand output format coverage per user requests.
- The Data Curation Portal [link] supports upload of published force-field data with appropriate metadata descriptors to support provenance based data sharing. New datasets may be curated interactively or using a python based toolset to upload large datasets en masse. Data curation requires an authorized account.
- The initial release of the repository features three integrated XML schemas:
- Class I organic force-fields in such as OPLS, Amber and CHARMM style representations
- Class II style force-fields such as CFF, PCFF, COMPASS and TEAMFF
- Coarse-Grained models at various levels of granularity
- For questions, comments and requests please contact: webff@nist.gov
If you use data from WebFF in your work, we ask that you please cite the following:
- The main source or the data cited in the XML metadata
- Frederick R. Phelan Jr., Kathleen Mullin, Pablo Garcia Beltran, Gule Teri, Priyanshu Mishra and Huai Sun, “The Web Force-Field (WebFF) Project: Ontology Based Force-Field Repository for Soft Materials at Multiple Levels of Granularity,” in preparation (2018).
External Resources¶
| WebFF-Documentation |  |
| Materials Data Curation System (MDCS) | |
Force-Field Data Search¶
XML Schemas¶
Class 1 Organic Force-Fields¶
Class 2 Organic Force-Fields¶
Coarse-Grained Force-Fields¶
Water Models¶
Python Tools¶
WebFF.py Module¶
WebFF Data Input: Excel to XML¶
WebFF Data Output Tools: XML to MD Format¶
Module Index¶
This module contains functions that translate data between Excel, XML, and molecular dynamics text formats
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WebFF.ReadExcelAnglePotential_CHARMM(sheet, sub_root)¶ Reads in the AnglePotential-CHARMM sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAnglePotential_COS2(sheet, sub_root)¶ Reads in the AnglePotential-COS2 sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAnglePotential_Class2(sheet, sub_root)¶ Reads in the AnglePotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAnglePotential_Cosine(sheet, sub_root)¶ Reads in the AnglePotential-Cosine sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAnglePotential_Harmonic(sheet, sub_root)¶ Reads in the AnglePotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAnglePotential_Tabular(sheet, sub_root)¶ Reads in the AnglePotential-Tabular sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAtomTypeAttributes(sheet, root)¶ Reads in the Atom-Types-Attributes sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAtomTypeAttributes_DFF(sheet, root)¶ Reads in the Atom-Attributes-DFF sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAtomTypeAttributes_Generic(sheet, root)¶ Reads in the Atom-Attributes-Generic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAtomTypes(sheet, root)¶ Reads in the Atom-Types sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAtomTypes_ATDL(sheet, root)¶ Reads in the AtomTypes-ATDL sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAtomTypes_CoarseGrained(sheet, root)¶ Reads in the AtomTypes-ATDL sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAtomTypes_DFF(sheet, root)¶ Reads in the AtomTypes-DFF sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAtomTypes_Generic(sheet, root)¶ Reads in the AtomTypes-Generic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelAutoEquivalenceTable(sheet, sub_root)¶ Reads in the Equivalence-Table sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelBondIncrements(sheet, sub_root)¶ Reads in the Bond-Increments sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelBondPotential_Class2(sheet, sub_root)¶ Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelBondPotential_FENE(sheet, sub_root)¶ Reads in the BondPotential-FENE sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelBondPotential_Harmonic(sheet, sub_root)¶ Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelBondPotential_Morse(sheet, sub_root)¶ Reads in the BondPotential-Morse sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelBondPotential_Quartic(sheet, sub_root)¶ Reads in the BondPotential-Quartic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelBondPotential_Tabular(sheet, sub_root)¶ Reads in the BondPotential-Tabular sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelCrossPotential_AngleAngle(sheet, sub_root)¶ Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelCrossPotential_AngleAngleTorsion(sheet, sub_root)¶ Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelCrossPotential_AngleTorsion(sheet, sub_root)¶ Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelCrossPotential_BondAngle(sheet, sub_root)¶ Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelCrossPotential_BondBond(sheet, sub_root)¶ Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelCrossPotential_BondBond13(sheet, sub_root)¶ Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelCrossPotential_EndBondTorsion(sheet, sub_root)¶ Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelCrossPotential_MiddleBondTorsion(sheet, sub_root)¶ Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelDihedralPotential_CHARMM(sheet, sub_root)¶ Reads in the DihedralPotential-CHARMM sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelDihedralPotential_Class2(sheet, sub_root)¶ Reads in the DihedralPotential-CHARMM sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelDihedralPotential_Fourier(sheet, sub_root)¶ Reads in the DihedralPotential-Fourier sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelDihedralPotential_FourierSimple(sheet, sub_root)¶ Reads in the DihedralPotential-FourierSimple sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelDihedralPotential_Harmonic(sheet, sub_root)¶ Reads in the DihedralPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelDihedralPotential_Multiharmonic(sheet, sub_root)¶ Reads in the DihedralPotential-Multiharmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelDihedralPotential_OPLS(sheet, sub_root)¶ Reads in the DihedralPotential-OPLS sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelDihedralPotential_Quadratic(sheet, sub_root)¶ Reads in the DihedralPotential-Quadratic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelDihedralPotential_Tabular(sheet, sub_root)¶ Reads in the DihedralPotential-Tabular sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelDissipativePotential_Langevin(sheet, sub_root)¶ Reads in the DissipativePotential-Langevin sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelEquivalenceTable(sheet, sub_root)¶ Reads in the Equivalence-Table sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelImproperPotential_CHARMM(sheet, sub_root)¶ Reads in the ImporperPotential-CHARMM sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelImproperPotential_COS2(sheet, sub_root)¶ Reads in the ImporperPotential-COS2 sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelImproperPotential_CVFF(sheet, sub_root)¶ Reads in the ImproperPotential-CVFF sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelImproperPotential_Class2(sheet, sub_root)¶ Reads in the ImporperPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelImproperPotential_Fourier(sheet, sub_root)¶ Reads in the ImporperPotential-Fourier sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelImproperPotential_Harmonic(sheet, sub_root)¶ Reads in the ImporperPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelImproperPotential_Umbrella(sheet, sub_root)¶ Reads in the ImporperPotential-Umbrella sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelMetaData_Header(sheet, sub_root)¶ Reads in the MetaData sheet from the WebFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelMetaData_Keywords(sheet, root)¶ Reads in the Keywords sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelMetaData_References(sheet, root)¶ Reads in the Keywords sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_EnergyRenorm(sheet, sub_root)¶ Reads in the NonBondPotential-EnergyRenorm sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_LJ(sheet, sub_root)¶ Reads in the NonBondPotential-LJ sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_LJ2(sheet, sub_root)¶ Reads in the NonBondPotential-LJ2 sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_LJ2AB(sheet, sub_root)¶ Reads in the NonBondPotential-LJ2AB sheet from the WebFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_LJ96(sheet, sub_root)¶ Reads in the NonBondPotential-LJRmin sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_LJ962(sheet, sub_root)¶ Reads in the NonBondPotential-LJ962 sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_LJAB(sheet, sub_root)¶ Reads in the NonBondPotential-LJAB sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_LJClass2(sheet, sub_root)¶ Reads in the NonBondPotential-LJClass2 sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_LJGROMACS(sheet, sub_root)¶ Reads in the NonBondPotential-LJ-GROMACS sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_LJRmin(sheet, sub_root)¶ Reads in the NonBondPotential-LJRmin sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_Mie(sheet, sub_root)¶ Reads in the NonBondPotential-Mie sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_Tabular(sheet, sub_root)¶ Reads in the NonBondPotential-Tabular sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelNonBondPotential_WCA(sheet, sub_root)¶ Reads in the NonBondPotential-WCA sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelRelationTree_DFF(sheet, root)¶ Reads in the RelationTree-DFF sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelSoftPotential_DPD(sheet, sub_root)¶ Reads in the SoftPotential-DPD sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelSoftPotential_SRP(sheet, sub_root)¶ Reads in the SoftPotential-SRP sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelWaterPotential_3Site(sheet, sub_root)¶ Reads in the WaterPotential-3Site sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelWaterPotential_4Site(sheet, sub_root)¶ Reads in the WaterPotential-4Site sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.ReadExcelWaterPotential_5Site(sheet, sub_root)¶ Reads in the WaterPotential-5Site sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.
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WebFF.XMLToFrcNonBondPotential_Class2(root, output_file)¶
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WebFF.XMLToFrcNonBondPotential_LJ2_AB(root, output_file)¶
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WebFF.XMLToFrcNonBondPotential_LJ_AB(root, output_file)¶
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WebFF.XMLToFrcNonBondPotential_LJ_GROMACS(root, output_file)¶
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WebFF.XMLToFrcNonBondPotential_LJ_Rmin(root, output_file)¶
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WebFF.XMLToFrcNonBondPotential_Weeks_Chandler_Anderson(root, output_file)¶
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WebFF.XMLToParamsAnglePotential_CHARMM(root, output_file)¶
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WebFF.XMLToParamsAnglePotential_COS2(root, output_file)¶
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WebFF.XMLToParamsAnglePotential_Class2(root, output_file)¶
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WebFF.XMLToParamsAnglePotential_Cosine(root, output_file)¶
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WebFF.XMLToParamsAnglePotential_Harmonic(root, output_file)¶
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WebFF.XMLToParamsAtomTypes(root, output_file)¶
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WebFF.XMLToParamsBondPotential_Harmonic(root, output_file)¶
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WebFF.XMLToParamsBondPotential_Morse(root, output_file)¶
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WebFF.XMLToParamsDihedralPotential_CHARMM(root, output_file)¶
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WebFF.XMLToParamsDihedralPotential_Class2(root, output_file)¶
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WebFF.XMLToParamsDihedralPotential_Fourier(root, output_file)¶
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WebFF.XMLToParamsDihedralPotential_FourierSimple(root, output_file)¶
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WebFF.XMLToParamsDihedralPotential_Harmonic(root, output_file)¶
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WebFF.XMLToParamsDihedralPotential_Multiharmonic(root, output_file)¶
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WebFF.XMLToParamsDihedralPotential_OPLS(root, output_file)¶
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WebFF.XMLToParamsDihedralPotential_Quadratic(root, output_file)¶
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WebFF.XMLToParamsImproperPotential_CHARMM(root, output_file)¶
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WebFF.XMLToParamsImproperPotential_COS2(root, output_file)¶
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WebFF.XMLToParamsImproperPotential_CVFF(root, output_file)¶
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WebFF.XMLToParamsImproperPotential_Class2(root, output_file)¶
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WebFF.XMLToParamsImproperPotential_Fourier(root, output_file)¶
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WebFF.XMLToParamsImproperPotential_Harmonic(root, output_file)¶
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WebFF.XMLToParamsImproperPotential_Umbrella(root, output_file)¶
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WebFF.XMLToParamsNonBondPotential_Class2(root, output_file)¶
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WebFF.XMLToParamsNonBondPotential_EnergyRenorm(root, output_file)¶
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WebFF.XMLToParamsNonBondPotential_LJ(root, output_file)¶
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WebFF.XMLToParamsNonBondPotential_LJ2(root, output_file)¶
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WebFF.XMLToParamsNonBondPotential_LJ2_AB(root, output_file)¶
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WebFF.XMLToParamsNonBondPotential_LJ96(root, output_file)¶
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WebFF.XMLToParamsNonBondPotential_LJ_AB(root, output_file)¶
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WebFF.XMLToParamsNonBondPotential_LJ_GROMACS(root, output_file)¶
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WebFF.XMLToParamsNonBondPotential_LJ_Rmin(root, output_file)¶
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WebFF.XMLToParamsNonBondPotential_Mie(root, output_file)¶
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WebFF.XMLToParamsNonBondPotential_Soft(root, output_file)¶
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WebFF.XMLToTableAnglePotential_Tabular(root, output_file)¶
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WebFF.XMLToTableBondPotential_Tabular(root, output_file)¶
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WebFF.XMLToTableDihedralPotential_Tabular(root, output_file)¶
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WebFF.XMLToTableNonBondPotential_Tabular(root, output_file)¶
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WebFF.XMLtoCitBib(root, output_file)¶
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WebFF.XMLtoFrcAnglePotential_CHARMM(root, output_file)¶
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WebFF.XMLtoFrcAnglePotential_COS2(root, output_file)¶
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WebFF.XMLtoFrcAnglePotential_Class2(root, output_file)¶
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WebFF.XMLtoFrcAnglePotential_Cosine(root, output_file)¶
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WebFF.XMLtoFrcAnglePotential_Harmonic(root, output_file)¶
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WebFF.XMLtoFrcAtomTypes(root, output_file)¶
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WebFF.XMLtoFrcAtomTypesCG(root, output_file)¶
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WebFF.XMLtoFrcBondIncrements(root, output_file)¶
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WebFF.XMLtoFrcBondPotential_Class2(root, output_file)¶
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WebFF.XMLtoFrcBondPotential_FENE(root, output_file)¶
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WebFF.XMLtoFrcBondPotential_Harmonic(root, output_file)¶
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WebFF.XMLtoFrcBondPotential_Morse(root, output_file)¶
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WebFF.XMLtoFrcCrossPotential_AngleAngle(root, output_file)¶
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WebFF.XMLtoFrcCrossPotential_AngleAngleTorsion(root, output_file)¶
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WebFF.XMLtoFrcCrossPotential_AngleTorsion(root, output_file)¶
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WebFF.XMLtoFrcCrossPotential_BondAngle(root, output_file)¶
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WebFF.XMLtoFrcCrossPotential_BondBond(root, output_file)¶
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WebFF.XMLtoFrcCrossPotential_BondBond13(root, output_file)¶
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WebFF.XMLtoFrcCrossPotential_EndBondTorsion(root, output_file)¶
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WebFF.XMLtoFrcCrossPotential_MiddleBondTorsion(root, output_file)¶
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WebFF.XMLtoFrcDihedralPotential_CHARMM(root, output_file)¶
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WebFF.XMLtoFrcDihedralPotential_Class2(root, output_file)¶
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WebFF.XMLtoFrcDihedralPotential_Fourier(root, output_file)¶
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WebFF.XMLtoFrcDihedralPotential_FourierSimple(root, output_file)¶
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WebFF.XMLtoFrcDihedralPotential_Harmonic(root, output_file)¶
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WebFF.XMLtoFrcDihedralPotential_Multiharmonic(root, output_file)¶
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WebFF.XMLtoFrcDihedralPotential_OPLS(root, output_file)¶
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WebFF.XMLtoFrcDihedralPotential_Quadratic(root, output_file)¶
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WebFF.XMLtoFrcEquivalenceTable(root, output_file)¶
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WebFF.XMLtoFrcImproperPotential_CHARMM(root, output_file)¶
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WebFF.XMLtoFrcImproperPotential_COS2(root, output_file)¶
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WebFF.XMLtoFrcImproperPotential_CVFF(root, output_file)¶
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WebFF.XMLtoFrcImproperPotential_Class2(root, output_file)¶
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WebFF.XMLtoFrcImproperPotential_Fourier(root, output_file)¶
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WebFF.XMLtoFrcImproperPotential_FourierSimple(root, output_file)¶
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WebFF.XMLtoFrcImproperPotential_Harmonic(root, output_file)¶
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WebFF.XMLtoFrcImproperPotential_Umbrella(root, output_file)¶
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WebFF.XMLtoFrcNonBondPotential_EnergyRenorm(root, output_file)¶
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WebFF.XMLtoFrcNonBondPotential_LJ(root, output_file)¶
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WebFF.XMLtoFrcNonBondPotential_LJ2(root, output_file)¶
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WebFF.XMLtoFrcNonBondPotential_LJ96(root, output_file)¶
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WebFF.XMLtoFrcNonBondPotential_Mie(root, output_file)¶
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WebFF.XMLtoFrcNonBondPotential_Soft(root, output_file)¶
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WebFF.XMLtoParamsBondPotential_Class2(root, output_file)¶
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WebFF.XMLtoParamsBondPotential_FENE(root, output_file)¶
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WebFF.XMLtoParamsCrossPotential_AngleAngle(root, output_file)¶
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WebFF.XMLtoParamsCrossPotential_AngleAngleTorsion(root, output_file)¶
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WebFF.XMLtoParamsCrossPotential_AngleTorsion(root, output_file)¶
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WebFF.XMLtoParamsCrossPotential_BondAngle(root, output_file)¶
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WebFF.XMLtoParamsCrossPotential_BondBond(root, output_file)¶
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WebFF.XMLtoParamsCrossPotential_BondBond13(root, output_file)¶
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WebFF.XMLtoParamsCrossPotential_EndBondTorsion(root, output_file)¶
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WebFF.XMLtoParamsCrossPotential_MiddleBondTorsion(root, output_file)¶
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WebFF.XMLtoParamsNonBondPotential_Weeks_Chandler_Anderson(root, output_file)¶
Tutorial¶
Data Curation for Atomistic Force-Field Data¶
References¶
- Jiří Vymětal and Jiří Vondrášek, “Parametrization of 2,2,2-Trifluoroethanol Based on the Generalized Amber Force Field Provides Realistic Agreement between Experimental and Calculated Properties of Pure Liquid as Well as Water-Mixed Solutions”, J. Phys. Chem. B, 118 (35), pp 10390–10404, (2014).
Data Curation for Coarse-Grained Force-Field Data¶
The Martini Coarse-Grained Force-Field¶
In this tutorial, we show step by step how to curate data for the Martini Coarse-Grained Force-Field into WebFF using the WebFF Excel data template and the WebFF.py Python library.
The data for the Martini force-field was ported to the Excel spreadsheet called: WebFF-DocumentationXMLCoarse-GrainedWebFF-CoarseGrained-DataTemplate.xlsx
There are three sections of Metadata to include
The atom types for Martini are general in nature, and each entry can stand for a number of similar but related chemical moeities.
References¶
- Siewert J. Marrink, H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, and Alex H. de Vries, “The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations,” J. Phys. Chem. B, 111 (27), pp 7812–7824, (2007).
- Martini v2.2 Force-Field Parameters, http://www.cgmartini.nl/images/parameters/ITP/martini_v2.2.itp
Publications¶
This page will attempt to keep an up-to-date listing of the papers which either use WebFF or used data from WebFF.
WebFF References¶
- Frederick R. Phelan Jr., Kathleen Mullin, Pablo Garcia Beltran, Gule Teri, Priyanshu Mishra and Huai Sun, “The Web Force-Field (WebFF) Project: Ontology Based Force-Field Repository for Soft Materials at Multiple Levels of Granularity,” in preparation (2018).
WebFF Data Publications¶
Coming Soon
Contacts¶
- WebFF Help
- Dr. Frederick R. Phelan Jr., NIST
- NIST Home Page, GitHub
- Prof. Huai Sun, Shanghai Jiao Tong University
- Group Home Page, Department Home Page
Legal¶
NIST Disclaimer¶
Any identification of commercial or open-source software in this document is done so purely in order to specify the methodology adequately. Such identification is not intended to imply recommendation or endorsement by the National Institute of Standards and Technology, nor is it intended to imply that the softwares identified are necessarily the best available for the purpose.
NIST Terms of Service (WebFF)¶
- As a user and/or an account holder on the NIST WebFF Repository, I understand that my actions and data on the system are subject to the following terms of use:
- The NIST WebFF Repository is a United States Government resource, and will only be used in support of the sharing and dissemination of scientific data.
- Data uploaded to this system are presented to users in as-provided condition. NIST makes no claims about the utility, veracity, or reliability of data on this system.
- Content uploaded to this server will be available to the general public, under suitable license terms selected by the provider. The server will advise downloaders of the license status of hosted content, but NIST takes no responsibility for license enforcement. This is the responsibility of the original data provider.
- Content that is part of invitation-only collections or communities will be protected by available technological mechanisms associated with the repository software. NIST does not guarantee that these protection mechanisms will prevent all forms of unauthorized access. Content requiring more stringent guarantees of protection should not be stored on this system.
- If data community administrators determine that content uploaded to this server does not contribute to the scientific data dissemination and discovery mission, which is the purpose of this server, the content may be removed without notice.
- While every effort is made to ensure the integrity of data deposited on the NIST WebFF Repository, NIST does not guarantee data integrity on this system.
- Accounts are assigned to single users. Account holders may not share account credentials with others, or allow others to access their sessions, except system operators, who may require such access for maintenance purposes.
- A user who has submitting or administrative rights to the system and who abuses their authority, or has some change in status that disqualifies them for the role, can have their submitter or administrative rights revoked by NIST management.
- NIST may monitor system activities or view data uploaded to the server, and may disclose these activities or data for any lawful Government purpose.
- NIST remains committed to the operation of public data repositories. NIST may discontinue this service at any time in favor of superior options. Any anticipated discontinuation of service will be announced in advance.
NIST License (WebFF.py)¶
This software was developed by employees of the National Institute of Standards and Technology (NIST), an agency of the Federal Government and is being made available as a public service. Pursuant to title 17 United States Code Section 105, works of NIST employees are not subject to copyright protection in the United States. This software may be subject to foreign copyright. Permission in the United States and in foreign countries, to the extent that NIST may hold copyright, to use, copy, modify, create derivative works, and distribute this software and its documentation without fee is hereby granted on a non-exclusive basis, provided that this notice and disclaimer of warranty appears in all copies.
THE SOFTWARE IS PROVIDED ‘AS IS’ WITHOUT ANY WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SOFTWARE WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND FREEDOM FROM INFRINGEMENT, AND ANY WARRANTY THAT THE DOCUMENTATION WILL CONFORM TO THE SOFTWARE, OR ANY WARRANTY THAT THE SOFTWARE WILL BE ERROR FREE. IN NO EVENT SHALL NIST BE LIABLE FOR ANY DAMAGES, INCLUDING, BUT NOT LIMITED TO, DIRECT, INDIRECT, SPECIAL OR CONSEQUENTIAL DAMAGES, ARISING OUT OF, RESULTING FROM, OR IN ANY WAY CONNECTED WITH THIS SOFTWARE, WHETHER OR NOT BASED UPON WARRANTY, CONTRACT, TORT, OR OTHERWISE, WHETHER OR NOT INJURY WAS SUSTAINED BY PERSONS OR PROPERTY OR OTHERWISE, AND WHETHER OR NOT LOSS WAS SUSTAINED FROM, OR AROSE OUT OF THE RESULTS OF, OR USE OF, THE SOFTWARE OR SERVICES PROVIDED HEREUNDER.
Metadata¶
Force-Field Protocol¶
Force-Field Name¶
Description¶
Data-Source¶
Keywords¶
Additional Keywords¶
WebFF-Scribe¶
Additional References¶
Attachments¶
Atom Types¶
Atom Type - ATDL¶
XML Schema¶
The XML schema for the Atom Type - ATDL has the following representation (design mode representation using Liquid XML Studio):
The general attributes (describing the entire set of atoms) are given by:
| General Attributes | Cardinality | Value/Definition |
| Nomenclature | Fixed | ATDL |
| comment | Optional | Comment attached to set of atoms |
The specific attributes (attached to each atom description) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| Description | Required | Description of the atom |
| Element | Required | Corresponding element of the atom |
| AtomicNumber | Required | Corresponding atomic number of the atom |
| AtomicMass | Required | Corresponding atomic mass of the atom |
The specific elements (contained within each instance of the atom template) are given by:
| Specific Elements | Cardinality | Value/Definition |
| AtomType-Name | Required | Atom type name |
| Atom | Required | Atom |
| BondedAtoms | Required | Bonded atoms |
| FormalCharge | Optional | Formal charge of the atom |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Atom Type - DFF¶
XML Schema¶
The XML schema for the Atom Type - DFF has the following representation (design mode representation using Liquid XML Studio):
The general attributes (describing the entire set of atoms) are given by:
| General Attributes | Cardinality | Value/Definition |
| Nomenclature | Fixed | DFF |
| comment | Optional | Comment attached to set of atoms |
The general elements (describing the entire set of atoms) are given by:
| General Attributes | Cardinality | Value/Definition |
| DFFRelationTree | Optional | Multiline DFF relation tree |
The specific attributes (attached to each atom description) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| Description | Required | Description of the atom |
| Element | Required | Corresponding element of the atom |
| AtomicNumber | Required | Corresponding atomic number of the atom |
| AtomicMass | Required | Corresponding atomic mass of the atom |
The specific elements (contained within each instance of the atom template) are given by:
| Specific Elements | Cardinality | Value/Definition |
| AtomType-Name | Required | Atom type name |
| Substructure | Required | Atom |
| Index | Required | Index of atom entry |
| Coordination | Optional | Coordination of the atom |
| Ringsize | Optional | Ringsize of the atom |
| Aromatic | Optional | Aromatic (true/false) |
| FormalCharge | Optional | Formal charge of the atom |
| ElementsAllowed | Optional | Elements allowed in the atom |
| ElementsDisallowed | Optional | Elements disallowed in the atom |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Atom Type - Generic¶
XML Schema¶
The XML schema for the Atom Type - Generic has the following representation (design mode representation using Liquid XML Studio):
The general attributes (describing the entire set of atoms) are given by:
| General Attributes | Cardinality | Value/Definition |
| Nomenclature | Fixed | Generic |
| comment | Optional | Comment attached to set of atoms |
The specific attributes (attached to each atom description) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| Description | Required | Description of the atom |
| Element | Required | Corresponding element of the atom |
| AtomicNumber | Required | Corresponding atomic number of the atom |
| AtomicMass | Required | Corresponding atomic mass of the atom |
The specific elements (contained within each instance of the atom template) are given by:
| Specific Elements | Cardinality | Value/Definition |
| AtomType-Name | Required | Atom type name |
| BondPattern | Required | Atom |
| Index | Required | Index of atom entry |
| BondOrder | Optional | Coordination of the atom |
| Ring | Optional | Ringsize of the atom |
| Aromatic | Optional | Aromatic (true/false) |
| FormalCharge | Optional | Formal charge of the atom |
| Hybridization | Optional | Hybridization of the atom |
| ElementsAllowed | Optional | Elements allowed in the atom |
| ElementsDisallowed | Optional | Elements disallowed in the atom |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Atom Type - Coarse Grained¶
XML Schema¶
The XML schema for the Atom Type - Coarse Grained has the following representation (design mode representation using Liquid XML Studio):
The general attributes (describing the entire set of atoms) are given by:
| General Attributes | Cardinality | Value/Definition |
| Nomenclature | Fixed | SMILES | SMARTS | CurlySMILES | SLN | InChi |
| comment | Optional | Comment attached to set of atoms |
The specific attributes (attached to each atom description) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| Description | Required | Description of the atom |
| AtomicMass-CG | Required | Corresponding atomic mass of the atom |
| AtomicMSize-CG | Required | Corresponding atomic size of the atom |
The specific elements (contained within each instance of the atom template) are given by:
| Specific Elements | Cardinality | Value/Definition |
| CG-Name | Required | Atom type name |
| CG_chemistry | Optional | Chemistry of the atom |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Bond Potentials¶
Class2 Bond¶
Functional Form¶
The class 2 bond potential has the functional form:
\(E={{K}_{2,ij}}{{\left( {{R}_{ij}}-{{R}_{0,ij}} \right)}^{2}}+{{K}_{3,ij}}{{\left( {{R}_{ij}}-{{R}_{0,ij}} \right)}^{3}}+{{K}_{4,ij}}{{\left( {{R}_{ij}}-{{R}_{0,ij}} \right)}^{4}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{2,ij}\) | Bond coefficient for atoms [i,j] (quadratic term) | energy/length^2 |
| \(K_{3,ij}\) | Bond coefficient for atoms [i,j] (cubic term) | energy/length^3 |
| \(K_{4,ij}\) | Bond coefficient for atoms [i,j] (quartic term) | energy/length^4 |
| \(R_{0,ij}\) | Equilibrium bond length for atoms [i,j] | length |
XML Schema¶
The XML schema for the class 2 bond potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Bond coefficient for atoms [i,j] (quadratic term) | \(K_{2,ij}\) | K2 |
| Bond coefficient for atoms [i,j] (cubic term) | \(K_{3,ij}\) | K3 |
| Bond coefficient for atoms [i,j] (quartic term) | \(K_{4,ij}\) | K4 |
| Equilibrium bond length for atoms [i,j] | \(R_{0,ij}\) | R0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Class2 |
| formula | Fixed | K2*(R-R0)^2+K3*(R-R0)^3+K4*(R-R0)^4 |
| K-units | Required | Enumerations specified in schema |
| R0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
FENE Bond¶
Functional Form¶
The FENE bond potential has the functional form:
\(E=-\frac{1}{2}{{K}_{ij}}R_{0,ij}^{2}\ln \left[ 1-{{\left( \frac{{{R}_{ij}}}{{{R}_{0,ij}}} \right)}^{2}} \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{ij}\) | Bond coefficient for atoms [i,j] | energy/length^2 |
| \(R_{0,ij}\) | Equilibrium bond length for atoms [i,j] | length |
XML Schema¶
The XML schema for the FENE bond potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Bond coefficient for atoms [i,j] | \(K_{ij}\) | K |
| Equilibrium bond length for atoms [i,j] | \(R_{0,ij}\) | R0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | FENE |
| formula | Fixed | -[(K*R0^2)/2]*ln[1-(R/R0)^2] |
| K-units | Required | Enumerations specified in schema |
| R0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Harmonic Bond¶
Functional Form¶
The harmonic bond potential has the functional form:
\(E = {K_{ij}} \cdot \left( {{R_{ij}} - {R_{0,ij}}} \right)^{2}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{ij}\) | Bond coefficient for atoms [i,j] | energy/length^2 |
| \(R_{0,ij}\) | Equilibrium bond length for atoms [i,j] | length |
XML Schema¶
The XML schema for the harmonic bond potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Bond coefficient for atoms [i,j] | \(K_{ij}\) | K |
| Equilibrium bond length for atoms [i,j] | \(R_{0,ij}\) | R0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Harmonic |
| formula | Fixed | K*(R_R0)^2 |
| K-units | Required | Enumerations specified in schema |
| R0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Morse Bond¶
Functional Form¶
The Morse bond potential has the functional form:
\(E=D{{\left[ 1-{{e}^{-\alpha ({{R}_{ij}}-{{R}_{0,ij}})}} \right]}^{2}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(D\) | Depth of the potential well | energy |
| \(\alpha\) | Stiffness parameter | inverse length |
| \(R_{0,ij}\) | Equilibrium bond length for atoms [i,j] | length |
XML Schema¶
The XML schema for the Morse bond potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Depth of the potential well | \(D\) | D |
| Stiffness parameter | \(\alpha\) | A |
| Equilibrium bond length for atoms [i,j] | \(R_{0,ij}\) | R0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Morse |
| formula | Fixed | D*[(1-exp(-A(R-R0))]^2 |
| D-units | Required | Enumerations specified in schema |
| A-units | Required | Enumerations specified in schema |
| R0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Tabular Bond¶
Tabular Form¶
The tabular bond potential has the parameters:
| Parameter | Parameter Definition | Units |
| N | Number of tabulated values | N/A |
| FP | Derivatives of the force at the innermost (fplo) and outermost (fphi) bond lengths | force/length |
| EQ | Equilibrium bond length | length |
The tabular bond potential has the tabulated values:
| index | bond-length | energy | force |
| i_1 | bl_1 | e_1 | f_1 |
| … | … | … | … |
| i_N | bl_N | e_n | f_N |
XML Schema¶
The XML schema for the tabular bond potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the parameters/symbols and XML schema notations are given by:
| Parameter Definition | Parameter/Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Section identifying keyword | N/A | keyword |
| Number of tabulated values | N | N |
| Derivative of the force at the innermost | FP | fplo |
| Derivative of the force at the outermost | FP | fphi |
| Equilibrium bond length | EQ | EQ |
| Index | index | index |
| Bond length | bond-length | bond-length |
| Energy | energy | energy |
| Force | force | force |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Tabular |
| bond-length-units | Required | Enumerations specified in schema |
| energy-units | Required | Enumerations specified in schema |
| force-units | Required | Enumerations specified in schema |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Angle Potentials¶
CHARMM Angle¶
Functional Form¶
The CHARMM angle potential has the functional form:
\(E={{K}_{a,ijk}}{{\left( {{\theta }_{ijk}}-{{\theta }_{0,ijk}} \right)}^{2}}+{{K}_{ub,ik}}{{\left( {{R}_{ik}}-{{R}_{ub,ik}} \right)}^{2}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{a,ijk}\) | Angle coefficient for atoms [i,j,k] | energy/degrees^2 |
| \(\theta_{0,ijk}\) | Equilibrium angle for atoms [i,j,k] | degrees |
| \(K_{ub,ik}\) | Coefficient for Urey-Bradley potential [i,k] | energy/length^2 |
| \(R_{ub,ik}\) | Equilibrium bond length for Urey-Bradley potential [i,k] | length |
XML Schema¶
The XML schema for the CHARMM angle potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Angle coefficient for atoms [i,j,k] | \(K_{a,ijk}\) | Ka |
| Equilibrium angle for atoms [i,j,k] | \(\theta_{0,ijk}\) | Theta0 |
| Coefficient for Urey-Bradley potential [i,k] | \(K_{ub,ik}\) | Kub |
| Equilibrium bond length for Urey-Bradley potential [i,k] | \(R_{ub,ik}\) | Rub |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | CHARMM |
| formula | Fixed | Ka*(Theta-Theta0)^2+Kub*(R-Rub)^2 |
| Ka-units | Required | Enumerations specified in schema |
| Theta0-units | Required | Enumerations specified in schema |
| Kub-units | Required | Enumerations specified in schema |
| Rub-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| precedence | Optional | Precedence of parameter set (where specified) |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Class2 Angle¶
Functional Form¶
The class 2 angle potential has the functional form:
\(E={{K}_{2,ijk}}{{\left( {{\theta }_{ijk}}-{{\theta }_{0,ijk}} \right)}^{2}}+{{K}_{3,ijk}}{{\left( {{\theta }_{ijk}}-{{\theta }_{0,ijk}} \right)}^{3}}+{{K}_{4,ijk}}{{\left( {{\theta }_{ijk}}-{{\theta }_{0,ijk}} \right)}^{4}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{2,ijk}\) | Angle coefficient for atoms [i,j,k] (quadratic term) | energy/degrees^2 |
| \(K_{3,ijk}\) | Angle coefficient for atoms [i,j,k] (cubic term) | energy/degrees^3 |
| \(K_{4,ijk}\) | Angle coefficient for atoms [i,j,k] (quartic term) | energy/degrees^4 |
| \(\theta_{0,ijk}\) | Equilibrium angle for atoms [i,j,k] | degrees |
XML Schema¶
The XML schema for the class 2 angle potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Angle coefficient for atoms [i,j,k] (quadratic term) | \(K_{2,ijk}\) | K2 |
| Angle coefficient for atoms [i,j,k] (cubic term) | \(K_{3,ijk}\) | K3 |
| Angle coefficient for atoms [i,j,k] (quartic term) | \(K_{4,ijk}\) | K4 |
| Equilibrium angle for atoms [i,j,k] | \(\theta_{0,ijk}\) | Theta0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Class2 |
| formula | Fixed | K2*(Theta-Theta0)^2+K3*(Theta-Theta0)^3+K4*(Theta-Theta0)^4 |
| K-units | Required | Enumerations specified in schema |
| Theta0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| precedence | Optional | Precedence of parameter set (where specified) |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
COS2 Angle¶
Functional Form¶
The COS2 angle potential has the functional form:
\(E={{K}_{a,ijk}}{{\left[ \cos \left( {{\theta }_{ijk}} \right)-\cos \left( {{\theta }_{0,ijk}} \right) \right]}^{2}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{a,ijk}\) | Angle coefficient for atoms [i,j,k] | energy |
| \(\theta_{0,ijk}\) | Equilibrium angle for atoms [i,j,k] | degrees |
XML Schema¶
The XML schema for the COS2 angle potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Angle coefficient for atoms [i,j,k] | \(K_{a,ijk}\) | Ka |
| Equilibrium angle for atoms [i,j,k] | \(\theta_{0,ijk}\) | Theta0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | cosine/squared |
| formula | Fixed | Ka*[cos(Theta)-cos(Theta0)]^2 |
| Ka-units | Required | Enumerations specified in schema |
| Theta0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| precedence | Optional | Precedence of parameter set (where specified) |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Cosine Angle¶
Functional Form¶
The cosine angle potential has the functional form:
\(E={{K}_{a,ijk}}\left[ 1+\cos \left( {{\theta }_{ijk}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{a,ijk}\) | Angle coefficient for atoms [i,j,k] | energy |
XML Schema¶
The XML schema for the cosine angle potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Angle coefficient for atoms [i,j,k] | \(K_{a,ijk}\) | Ka |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Cosine |
| formula | Fixed | Ka*[1+cos(theta)] |
| Ka-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| precedence | Optional | Precedence of parameter set (where specified) |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Harmonic Angle¶
Functional Form¶
The harmonic angle potential has the functional form:
\(E = {K_{a,ijk}} \cdot \left( {{\theta_{ijk}} - {\theta_{0,ijk}}} \right)^2\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{a,ijk}\) | Angle coefficient for atoms [i,j,k] | energy/degrees^2 |
| \(\theta_{0,ijk}\) | Equilibrium angle for atoms [i,j,k] | degrees |
XML Schema¶
The XML schema for the harmonic angle potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Angle coefficient for atoms [i,j,k] | \(K_{a,ijk}\) | Ka |
| Equilibrium angle for atoms [i,j,k] | \(\theta_{0,ijk}\) | Theta0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Harmonic |
| formula | Fixed | Ka*(Theta-Theta0)^2 |
| Ka-units | Required | Enumerations specified in schema |
| Theta0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| precedence | Optional | Precedence of parameter set (where specified) |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Tabular Angle¶
Tabular Form¶
The tabular angle potential has the parameters:
| Parameter | Parameter Definition | Units |
| N | Number of tabulated values | N/A |
| FP | Derivatives of the force at the innermost (fplo) and outermost (fphi) angles | force/angle |
| EQ | Equilibrium angle | angle |
The tabular angle potential has the tabulated values:
| index | angle | energy | derivative |
| i_1 | a_1 | e_1 | de_1 |
| … | … | … | … |
| i_N | a_N | e_n | de_N |
XML Schema¶
The XML schema for the tabular angle potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the parameters/symbols and XML schema notations are given by:
| Parameter Definition | Parameter/Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Section identifying keyword | N/A | keyword |
| Number of tabulated values | N | N |
| Derivative of the force at the innermost | FP | fplo |
| Derivative of the force at the outermost | FP | fphi |
| Equilibrium angle | EQ | EQ |
| Index | index | index |
| Angle | angle | angle |
| Energy | energy | energy |
| Derivate of energy | derivative | energy-diff |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Tabular |
| angle-units | Required | Enumerations specified in schema |
| energy-units | Required | Enumerations specified in schema |
| energy-diff-units | Required | Enumerations specified in schema |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Dihedral Potentials¶
CHARMM Dihedral¶
Functional Form¶
The CHARMM dihedral potential has the functional form:
\(E={{K}_{d,ijkl}}\left[ 1+\cos \left( N{{\phi }_{ijkl}}-{{\phi }_{0,ijkl}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{d,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(N\) | Nonnegative integer coefficient | N/A |
| \(\phi_{0,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
XML Schema¶
The XML schema for the CHARMM dihedral potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{d,ijkl}\) | Kd |
| Nonnegative integer coefficient | \(N\) | N |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(\phi_{0,ijkl}\) | Phi0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | CHARMM |
| formula | Fixed | Kd*[1+cos(N*Phi-Phi0)] |
| convention | Optional | Enumerations specified in schema |
| Kd-units | Required | Enumerations specified in schema |
| Phi0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Class 2 Dihedral¶
Functional Form¶
The class 2 dihedral potential has the functional form:
\(E={{K}_{1,ijkl}}\left[ 1-\cos \left( {{\phi }_{ijkl}}-{{\phi }_{1,ijkl}} \right) \right]+{{K}_{2,ijkl}}\left[ 1-\cos \left( 2{{\phi }_{ijkl}}-{{\phi }_{2,ijkl}} \right) \right]\) \(\qquad +{{K}_{3,ijkl}}\left[ 1-\cos \left( 3{{\phi }_{ijkl}}-{{\phi }_{3,ijkl}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{1,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{2,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{3,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(\phi_{1,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
| \(\phi_{2,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
| \(\phi_{3,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
XML Schema¶
The XML schema for the class 2 dihedral potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{1,ijkl}\) | K1 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{2,ijkl}\) | K2 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{3,ijkl}\) | K3 |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(\phi_{1,ijkl}\) | Phi1 |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(\phi_{2,ijkl}\) | Phi2 |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(\phi_{3,ijkl}\) | Phi3 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | Class2 |
| formula | Fixed | K1*[1-cos(Phi-Phi1)]+K2*[1-cos(2*Phi-Phi2)]+K3*[1-cos(3*Phi-Phi3)] |
| convention | Optional | Enumerations specified in schema |
| Kn-units | Required | Enumerations specified in schema |
| Phin-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Fourier Dihedral¶
Functional Form¶
The Fourier dihedral potential has the functional forms:
\(E={{K}_{1,ijkl}}\left[ 1+\cos \left( {{N}_{1}}{{\phi }_{ijkl}}-{{D}_{1,ijkl}} \right) \right]+{{K}_{2,ijkl}}\left[ 1+\cos \left( {{N}_{2}}{{\phi }_{ijkl}}-{{D}_{2,ijkl}} \right) \right]\) \(\qquad +{{K}_{3,ijkl}}\left[ 1+\cos \left( {{N}_{3}}{{\phi }_{ijkl}}-{{D}_{3,ijkl}} \right) \right]+{{K}_{4,ijkl}}\left[ 1+\cos \left( {{N}_{4}}{{\phi }_{ijkl}}-{{D}_{4,ijkl}} \right) \right]\) \(\qquad +{{K}_{5,ijkl}}\left[ 1+\cos \left( {{N}_{5}}{{\phi }_{ijkl}}-{{D}_{5,ijkl}} \right) \right]\)
\(E={{K}_{1,ijkl}}\left[ 1-\cos \left( {{N}_{1}}{{\phi }_{ijkl}}-{{D}_{1,ijkl}} \right) \right]+{{K}_{2,ijkl}}\left[ 1-\cos \left( {{N}_{2}}{{\phi }_{ijkl}}-{{D}_{2,ijkl}} \right) \right]\) \(\qquad +{{K}_{3,ijkl}}\left[ 1-\cos \left( {{N}_{3}}{{\phi }_{ijkl}}-{{D}_{3,ijkl}} \right) \right]+{{K}_{4,ijkl}}\left[ 1-\cos \left( {{N}_{4}}{{\phi }_{ijkl}}-{{D}_{4,ijkl}} \right) \right]\) \(\qquad +{{K}_{5,ijkl}}\left[ 1-\cos \left( {{N}_{5}}{{\phi }_{ijkl}}-{{D}_{5,ijkl}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{1,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{2,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{3,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{4,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{5,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(N_{1}\) | Nonnegative integer coefficient | N/A |
| \(N_{2}\) | Nonnegative integer coefficient | N/A |
| \(N_{3}\) | Nonnegative integer coefficient | N/A |
| \(N_{4}\) | Nonnegative integer coefficient | N/A |
| \(N_{5}\) | Nonnegative integer coefficient | N/A |
| \(D_{1,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
| \(D_{2,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
| \(D_{3,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
| \(D_{4,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
| \(D_{5,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
XML Schema¶
The XML schema for the Fourier dihedral potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{1,ijkl}\) | K1 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{2,ijkl}\) | K2 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{3,ijkl}\) | K3 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{4,ijkl}\) | K4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{5,ijkl}\) | K5 |
| Nonnegative integer coefficient | \(N_{1}\) | N1 |
| Nonnegative integer coefficient | \(N_{2}\) | N2 |
| Nonnegative integer coefficient | \(N_{3}\) | N3 |
| Nonnegative integer coefficient | \(N_{4}\) | N4 |
| Nonnegative integer coefficient | \(N_{5}\) | N5 |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(D_{1,ijkl}\) | D1 |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(D_{2,ijkl}\) | D2 |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(D_{3,ijkl}\) | D3 |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(D_{4,ijkl}\) | D4 |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(D_{5,ijkl}\) | D5 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | Fourier |
| formula | Fixed | Enumerations specified in schema |
| convention | Optional | Enumerations specified in schema |
| Kn-units | Required | Enumerations specified in schema |
| Dn-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Fourier (Simple) Dihedral¶
Functional Form¶
The Fourier (Simple) dihedral potential has the functional forms:
\(E={{K}_{1,ijkl}}\left[ 1+\cos \left( {{\phi }_{ijkl}} \right) \right]+{{K}_{2,ijkl}}\left[ 1+\cos \left( {{\phi }_{ijkl}} \right) \right]+{{K}_{3,ijkl}}\left[ 1+\cos \left( {{\phi }_{ijkl}} \right) \right]\) \(\qquad +{{K}_{4,ijkl}}\left[ 1+\cos \left( {{\phi }_{ijkl}} \right) \right]+{{K}_{5,ijkl}}\left[ 1+\cos \left( {{\phi }_{ijkl}} \right) \right]\)
\(E={{K}_{1,ijkl}}\left[ 1-\cos \left( {{\phi }_{ijkl}} \right) \right]+{{K}_{2,ijkl}}\left[ 1-\cos \left( {{\phi }_{ijkl}} \right) \right]+{{K}_{3,ijkl}}\left[ 1-\cos \left( {{\phi }_{ijkl}} \right) \right]\) \(\qquad +{{K}_{4,ijkl}}\left[ 1-\cos \left( {{\phi }_{ijkl}} \right) \right]+{{K}_{5,ijkl}}\left[ 1-\cos \left( {{\phi }_{ijkl}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{1,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{2,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{3,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{4,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{5,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
XML Schema¶
The XML schema for the Fourier (Simple) dihedral potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{1,ijkl}\) | K1 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{2,ijkl}\) | K2 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{3,ijkl}\) | K3 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{4,ijkl}\) | K4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{5,ijkl}\) | K5 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | Fourier |
| formula | Fixed | Enumerations specified in schema |
| convention | Optional | Enumerations specified in schema |
| Kn-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Harmonic Dihedral¶
Functional Form¶
The harmonic dihedral potential has the functional form:
\(E={{K}_{d,ijkl}}\left[ 1+{{N}_{s}}\cos \left( N{{\phi }_{ijkl}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{d,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(N_{s}\) | Determines sign convention (-1 or +1) | N/A |
| \(N\) | Nonnegative integer coefficient | N/A |
XML Schema¶
The XML schema for the harmonic dihedral potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{d,ijkl}\) | Kd |
| Determines sign convention (-1 or +1) | \(N_{S}\) | Ns |
| Nonnegative integer coefficient | \(N\) | N |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | Harmonic |
| formula | Fixed | Kd*[1+Ns*cos(N*Phi)] |
| convention | Optional | Enumerations specified in schema |
| Kd-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
OPLS Dihedral¶
Functional Form¶
The OPLS dihedral potential has the functional forms:
\(E=\frac{1}{2}{{K}_{1,ijkl}}\left[ 1+\cos \left( {{\phi }_{ijkl}} \right) \right]+\frac{1}{2}{{K}_{2,ijkl}}\left[ 1-\cos \left( 2{{\phi }_{ijkl}} \right) \right]+\frac{1}{2}{{K}_{3,ijkl}}\left[ 1+\cos \left( 3{{\phi }_{ijkl}} \right) \right]\) \(\qquad +\frac{1}{2}{{K}_{4,ijkl}}\left[ 1-\cos \left( 4{{\phi }_{ijkl}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{1,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{2,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{3,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{4,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
XML Schema¶
The XML schema for the OPLS dihedral potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{1,ijkl}\) | K1 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{2,ijkl}\) | K2 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{3,ijkl}\) | K3 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{4,ijkl}\) | K4 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | OPLS |
| formula | Fixed | 0.5*{K1*[1+cos(Phi)]+K2*[1-cos(2*Phi)]+K3*[1+cos(3*Phi)]+K4*[1-cos(4*Phi)]} |
| convention | Optional | Enumerations specified in schema |
| Kn-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Quadratic Dihedral¶
Functional Form¶
The quadratic dihedral potential has the functional form:
\(E = {K_{d,ijkl}} \cdot \left( {{\phi_{ijkl}} - {\phi_{0,ijkl}}} \right)^2\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{d,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy/degrees^2 |
| \(\phi_{0,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
XML Schema¶
The XML schema for the quadratic dihedral potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{d,ijkl}\) | Kd |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(\phi_{0,ijkl}\) | Phi0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | Quadratic |
| formula | Fixed | Kd*(Phi_Phi0)^2 |
| convention | Optional | Enumerations specified in schema |
| Kd-units | Required | Enumerations specified in schema |
| Phi0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Multi-Harmonic Dihedral¶
Functional Form¶
The Multi-Harmonic dihedral potential has the functional form:
\(E={{A}_{1,ijkl}}+{{A}_{2,ijkl}}\cos \left( {{\phi }_{ijkl}} \right) +{{A}_{3,ijkl}}{\cos}^{2}\left( {{\phi }_{ijkl}} \right) +{{A}_{4,ijkl}}{\cos}^{3}\left( {{\phi }_{ijkl}} \right) +{{A}_{5,ijkl}}{\cos}^{4}\left( {{\phi }_{ijkl}} \right)\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(A_{1,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(A_{2,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(A_{3,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(A_{4,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(A_{5,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
XML Schema¶
The XML schema for the Fourier dihedral potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(A_{1,ijkl}\) | A1 |
| Dihedral coefficient for atoms [i,j,k,l] | \(A_{2,ijkl}\) | A2 |
| Dihedral coefficient for atoms [i,j,k,l] | \(A_{3,ijkl}\) | A3 |
| Dihedral coefficient for atoms [i,j,k,l] | \(A_{4,ijkl}\) | A4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(A_{5,ijkl}\) | A5 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | Fourier |
| formula | Fixed | Enumerations specified in schema |
| convention | Optional | Enumerations specified in schema |
| An-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Tabular Dihedral¶
Tabular Form¶
The tabular dihedral potential has the parameters:
| Parameter | Parameter Definition | Units |
| N | Number of tabulated values | N/A |
| NOF | Allows omission of forces (energy derivatives) in the table | N/A |
| DEGREES | Specify degrees as units for the angles | N/A |
| RADIANS | Specify radians as units for the angles | N/A |
| CHECKU | File to save interpolated energy table | N/A |
| CHECKF | File to save interpolated force table | N/A |
The tabular dihedral potential has the tabulated values:
| index | angle | energy | derivative |
| i_1 | a_1 | e_1 | de_1 |
| … | … | … | … |
| i_N | a_N | e_n | de_N |
XML Schema¶
The XML schema for the tabular dihedral potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the parameters/symbols and XML schema notations are given by:
| Parameter Definition | Parameter/Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Section identifying keyword | N/A | keyword |
| Number of tabulated values | N | N |
| Allows omission of forces in the table | NOF | NOF |
| Specify degrees as units for the angles | DEGREES | angle-units |
| Specify radians as units for the angles | RADIANS | angle-units |
| File to save interpolated energy table | CHECKU | CHECKU |
| File to save interpolated force table | CHECKF | CHECKF |
| Index | index | index |
| Angle | angle | angle |
| Energy | energy | energy |
| Derivate of energy | derivative | energy-diff |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Tabular |
| angle-units | Required | Enumerations specified in schema |
| energy-units | Required | Enumerations specified in schema |
| energy-diff-units | Required | Enumerations specified in schema |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Improper Potentials¶
CHARMM Improper¶
Functional Form¶
The CHARMM improper potential has the functional forms:
\(E={{K}_{d,ijkl}}\left[ 1+\cos \left( N{{\phi }_{ijkl}}-{{\phi }_{0,ijkl}} \right) \right]\)
\(E={{K}_{d,ijkl}}\left[ 1+\cos \left( N{{\phi }_{ijkl}}+{{\phi }_{0,ijkl}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{d,ijkl}\) | Improper coefficient for atoms [i,j,k,l] | energy |
| \(N\) | Nonnegative integer coefficient | N/A |
| \(\phi_{0,ijkl}\) | Equilibrium improper angle for atoms [i,j,k,l] | degrees |
XML Schema¶
The XML schema for the CHARMM improper potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Improper coefficient for atoms [i,j,k,l] | \(K_{d,ijkl}\) | Kd |
| Nonnegative integer coefficient | \(N\) | N |
| Equilibrium improper angle for atoms [i,j,k,l] | \(\phi_{0,ijkl}\) | Phi0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | CHARMM |
| formula | Fixed | Kd*[1+cos(N*Phi-Phi0)], Kd*[1+cos(N*Phi+Phi0)] |
| convention | Optional | Enumerations specified in schema |
| Kd-units | Required | Enumerations specified in schema |
| Phi0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Class 2 Improper¶
Functional Form¶
The class 2 improper potential has the functional form:
\(E = {K_{i,ijkl}} \cdot \left( {{\chi_{ijkl}} - {\chi_{0,ijkl}}} \right)^2\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{i,ijkl}\) | Improper coefficient for atoms [i,j,k,l] | energy/degrees^2 |
| \(\chi_{0,ijkl}\) | Equilibrium improper angle for atoms [i,j,k,l] | degrees |
XML Schema¶
The XML schema for the class 2 improper potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Improper coefficient for atoms [i,j,k,l] | \(K_{i,ijkl}\) | Ki |
| Equilibrium improper angle for atoms [i,j,k,l] | \(\chi_{0,ijkl}\) | Chi0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | Class2 |
| formula | Fixed | Ki*(Chi-Chi0)^2 |
| convention | Optional | Enumerations specified in schema |
| Ki-units | Required | Enumerations specified in schema |
| Chi0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
COS2 Improper¶
Functional Form¶
The COS2 improper potential has the functional form:
\(E={{K}_{i,ijkl}}{{\cos }^{2}}\left( {{\chi }_{ijkl}}-{{\chi }_{0,ijkl}} \right)\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{i,ijkl}\) | Improper coefficient for atoms [i,j,k,l] | energy |
| \(\chi_{0,ijkl}\) | Equilibrium improper angle for atoms [i,j,k,l] | degrees |
XML Schema¶
The XML schema for the COS2 improper potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Improper coefficient for atoms [i,j,k,l] | \(K_{i,ijkl}\) | Ki |
| Equilibrium improper angle for atoms [i,j,k,l] | \(\chi_{0,ijkl}\) | Chi0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | cosine/squared |
| formula | Fixed | Ki*cos(Chi-Chi0)^2 |
| convention | Optional | Enumerations specified in schema |
| Ki-units | Required | Enumerations specified in schema |
| Chi0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
CVFF Improper¶
Functional Form¶
The CVFF improper potential has the functional form:
\(E={{K}_{i,ijkl}}\left[ 1+{{N}_{s}}\cos \left( N{{\phi }_{ijkl}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{i,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(N_{s}\) | Determines sign convention (-1 or +1) | N/A |
| \(N\) | Nonnegative integer coefficient | N/A |
XML Schema¶
The XML schema for the CVFF improper potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{i,ijkl}\) | K1 |
| Determines sign convention (-1 or +1) | \(N_{S}\) | Ns |
| Nonnegative integer coefficient | \(N\) | N |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | CVFF |
| formula | Fixed | Ki*[1+Ns*cos(N*Phi)] |
| convention | Optional | Enumerations specified in schema |
| Ki-units | Required | Enumerations specified in schema |
| Chi0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Fourier Improper¶
Functional Form¶
The Fourier improper potential has the functional form:
\(E={{K}_{i,ijkl}}\left[ {{C}_{0,ijkl}}+{{C}_{1,ijkl}}\cos \left( {{\omega }_{ijkl}} \right)+{{C}_{2,ijkl}}\cos \left( 2{{\omega }_{ijkl}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{i,ijkl}\) | Improper coefficient for atoms [i,j,k,l] | energy |
| \(C_{0,ijkl}\) | Real coefficient for cosine term #0 [i,j,k,l] | N/A |
| \(C_{1,ijkl}\) | Real coefficient for cosine term #1 [i,j,k,l] | N/A |
| \(C_{2,ijkl}\) | Real coefficient for cosine term #2 [i,j,k,l] | N/A |
XML Schema¶
The XML schema for the Fourier improper potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Improper coefficient for atoms [i,j,k,l] | \(K_{i,ijkl}\) | Ki |
| Real coefficient for cosine term #0 [i,j,k,l] | \(C_{0,ijkl}\) | C0 |
| Real coefficient for cosine term #1 [i,j,k,l] | \(C_{1,ijkl}\) | C1 |
| Real coefficient for cosine term #2 [i,j,k,l] | \(C_{2,ijkl}\) | C2 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | Fourier |
| formula | Fixed | Ki*[C0+C1*cos(w)+C2*cos(2*w)] |
| convention | Optional | Enumerations specified in schema |
| Ki-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Harmonic Improper¶
Functional Form¶
The harmonic improper potential has the functional form:
\(E = {K_{i,ijkl}} \cdot \left( {{\chi_{ijkl}} - {\chi_{0,ijkl}}} \right)^2\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{i,ijkl}\) | Improper coefficient for atoms [i,j,k,l] | energy/degrees^2 |
| \(\chi_{0,ijkl}\) | Equilibrium improper angle for atoms [i,j,k,l] | degrees |
XML Schema¶
The XML schema for the harmonic improper potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Improper coefficient for atoms [i,j,k,l] | \(K_{i,ijkl}\) | Ki |
| Equilibrium improper angle for atoms [i,j,k,l] | \(\chi_{0,ijkl}\) | Chi0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | Harmonic |
| formula | Fixed | Ki*(Chi-Chi0)^2 |
| convention | Optional | Enumerations specified in schema |
| Ki-units | Required | Enumerations specified in schema |
| Chi0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Umbrella Improper¶
Functional Form¶
The umbrella improper potential has the functional form:
\(E=\left\{ \begin{align} & \frac{1}{2}{{K}_{i,ijkl}}{{\left[ \frac{1+\cos \left( {{\omega }_{0,ijkl}} \right)}{\sin \left( {{\omega }_{0,ijkl}} \right)} \right]}^{2}}\left[ \cos \left( {{\omega }_{ijkl}} \right)-\cos \left( {{\omega }_{0,ijkl}} \right) \right],\text{ if }{{\omega }_{0,ijkl}}\ne 0 \\ & {{K}_{i,ijkl}}\left[ 1-\cos \left( {{\omega }_{ijkl}} \right) \right],\text{ if }{{\omega }_{0,ijkl}}=0 \\ \end{align} \right.\)
The force-field parameters for this potential and units are given by:
XML Schema¶
The XML schema for the umbrella improper potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Improper coefficient for atoms [i,j,k,l] | \(K_{i,ijkl}\) | Ki |
| Equilibrium improper angle for atoms [i,j,k,l] | \(\omega_{0,ijkl}\) | w0 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | Umbrella |
| formula | Fixed | 0.5*K*[{1+cos(w0)}/sin(w0)]^2*[cos(w)-cos(w0)], w0 ≠ 0°; K*[1-cos(w)], w0 = 0° |
| convention | Optional | Enumerations specified in schema |
| Ki-units | Required | Enumerations specified in schema |
| w0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Cross Potentials¶
Cross: Bond-Bond¶
Functional Form¶
The Bond-Bond Cross Potential has the functional form:
\(E = {M} \left( {{R_{ij}} - {R_{1,ij}}} \right) \left( {{R_{jk}} - {R_{2,jk}}} \right)\)
This term is part of the Class2 Angle Potential style.
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(M\) | Cross potential bond coefficient for atoms [i,j,k] | energy |
| \(R_{1,ij}\) | Equilibrium bond length for atoms [i,j] | length |
| \(R_{2,jk}\) | Equilibrium bond length for atoms [j,k] | length |
XML Schema¶
The XML schema for the Bond-Bond Cross Potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Bond coefficient for atoms [i,j,k] | \(M\) | M |
| Equilibrium bond length for atoms [i,j] | \(R_{1,ij}\) | R1 |
| Equilibrium bond length for atoms [j,k] | \(R_{2,jk}\) | R2 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | BondBond |
| formula | Fixed | M*(Rij-R1)*(Rjk-R2) |
| M-units | Required | Enumerations specified in schema |
| Ri-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Cross: Bond-Bond-13¶
Functional Form¶
The Bond-Bond-13 Cross Potential has the functional form:
\(E = {N} \left( {{R_{ij}} - {R_{1,ij}}} \right) \left( {{R_{kl}} - {R_{3,kl}}} \right)\)
This term is part of the Class2 Dihedral Potential style.
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(N\) | Cross potential bond coefficient for atoms [i,j,k,l] | energy |
| \(R_{1,ij}\) | Equilibrium bond length for atoms [i,j] | length |
| \(R_{3,kl}\) | Equilibrium bond length for atoms [k,l] | length |
XML Schema¶
The XML schema for the Bond-Bond-13 Cross Potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Bond coefficient for atoms [i,j,k,l] | \(N\) | N |
| Equilibrium bond length for atoms [i,j] | \(R_{1,ij}\) | R1 |
| Equilibrium bond length for atoms [k,l] | \(R_{3,kl}\) | R3 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | BondBond13 |
| formula | Fixed | N*(Rij-R1)*(Rkl-R3) |
| N-units | Required | Enumerations specified in schema |
| Ri-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Cross: Angle-Angle¶
Functional Form¶
The Angle-Angle Cross Potential has the functional form:
\(E={{M}_{1,ijkl}}\left( {{\theta }_{ijk}}-{{\theta }_{1,ijk}} \right)\left( {{\theta }_{kjl}}-{{\theta }_{1,kjl}} \right)+{{M}_{2,ijkl}}\left( {{\theta }_{ijk}}-{{\theta }_{1,ijk}} \right)\left( {{\theta }_{ijl}}-{{\theta }_{2,ijl}} \right)\) \(\qquad +{{M}_{3,ijkl}}\left( {{\theta }_{ijl}}-{{\theta }_{2,ijl}} \right)\left( {{\theta }_{kjl}}-{{\theta }_{1,kjl}} \right)\)
This term is part of the Class2 Improper Potential style.
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(M_{1,ijkl}\) | Cross potential angle coefficient for atoms [i,j,k,l] | energy |
| \(M_{2,ijkl}\) | Cross potential angle coefficient for atoms [i,j,k,l] | energy |
| \(M_{3,ijkl}\) | Cross potential angle coefficient for atoms [i,j,k,l] | energy |
| \({\theta }_{1,ijk}\) | Equilibrium angle for atoms [i,j,k] | degrees |
| \({\theta }_{2,ijl}\) | Equilibrium angle for atoms [i,j,l] | degrees |
| \({\theta }_{3,kjl}\) | Equilibrium angle for atoms [k,j,l] | degrees |
XML Schema¶
The XML schema for the Angle-Angle Cross Potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Cross potential angle coefficient for atoms [i,j,k,l] | \(M_{1,ijkl}\) | M1 |
| Cross potential angle coefficient for atoms [i,j,k,l] | \(M_{2,ijkl}\) | M2 |
| Cross potential angle coefficient for atoms [i,j,k,l] | \(M_{3,ijkl}\) | M3 |
| Equilibrium angle for atoms [i,j,k] | \({\theta }_{1,ijk}\) | Theta1 |
| Equilibrium angle for atoms [i,j,l] | \({\theta }_{2,ijl}\) | Theta2 |
| Equilibrium angle for atoms [k,j,l] | \({\theta }_{3,kjl}\) | Theta3 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | AngleAngle |
| formula | Fixed | M1*(Theta-Theta1)(Theta-Theta3)+M2*(Theta-Theta1)(Theta-Theta2)+M3*(Theta-Theta2)(Theta-Theta3) |
| M-units | Required | Enumerations specified in schema |
| Theta-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Cross: Bond-Angle¶
Functional Form¶
The Bond-Angle Cross Potential has the functional form:
\(E={{N}_{1,ijk}}\left( {{R}_{ij}}-{{R}_{1,ij}} \right)\left( {{\theta }_{ijk}}-{{\theta }_{0,ijk}} \right)+{{N}_{2,ijk}}\left( {{R}_{jk}}-{{R}_{2,jk}} \right)\left( {{\theta }_{ijk}}-{{\theta }_{0,ijk}} \right)\)
This term is part of the Class2 Angle Potential style.
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(N_{1,ijk}\) | Cross potential bond-angle coefficient for atoms [i,j,k] | energy/length/degrees |
| \(N_{2,ijk}\) | Cross potential bond-angle coefficient for atoms [i,j,k] | energy/length/degrees |
| \(R_{1,ij}\) | Equilibrium bond length for atoms [i,j] | length |
| \(R_{2,jk}\) | Equilibrium bond length for atoms [j,k] | length |
| \({\theta }_{0,ijk}\) | Equilibrium angle for atoms [i,j,k] | degrees |
XML Schema¶
The XML schema for the Bond-Angle Cross Potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Equilibrium angle for atoms [i,j,k] | \({\theta }_{0,ijk}\) | Theta0 |
| Cross potential bond-angle coefficient for atoms [i,j,k] | \(N_{1,ijk}\) | N1 |
| Cross potential bond-angle coefficient for atoms [i,j,k] | \(N_{2,ijk}\) | N2 |
| Equilibrium bond length for atoms [i,j] | \(R_{1,ij}\) | R1 |
| Equilibrium bond length for atoms [j,k] | \(R_{2,jk}\) | R2 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | BondAngle |
| formula | Fixed | N1*(R-R1)*(Theta-Theta0)+N2*(R-R2)*(Theta-Theta0) |
| N-units | Required | Enumerations specified in schema |
| Ri-units | Required | Enumerations specified in schema |
| Theta0-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Cross: Middle-Bond-Torsion¶
Functional Form¶
The Middle-Bond-Torsion Cross Potential has the functional form:
\(E=\left( {{R}_{jk}}-{{R}_{2,jk}} \right)\left[ {{A}_{1,ijkl}}\cos \left( {{\phi }_{ijkl}} \right)+{{A}_{2,ijkl}}\cos \left( 2{{\phi }_{ijkl}} \right)+{{A}_{3,ijkl}}\cos \left( 3{{\phi }_{ijkl}} \right) \right]\)
This term is part of the Class2 Dihedral Potential style.
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(A_{1,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/length |
| \(A_{2,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/length |
| \(A_{3,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/length |
| \(R_{2,jk}\) | Equilibrium bond length for atoms [j,k] | length |
XML Schema¶
The XML schema for the Middle-Bond-Torsion Cross Potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Cosine term coefficient for atoms [i,j,k,l] | \(A_{1,ijkl}\) | A1 |
| Cosine term coefficient for atoms [i,j,k,l] | \(A_{2,ijkl}\) | A2 |
| Cosine term coefficient for atoms [i,j,k,l] | \(A_{3,ijkl}\) | A3 |
| Equilibrium bond length for atoms [j,k] | \(R_{2,jk}\) | R2 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | MiddleBondTorsion |
| formula | Fixed | (R-R2)*[A1*cos(Phi)+A2*cos(2*Phi)+A3*cos(3*Phi)] |
| A-units | Required | Enumerations specified in schema |
| R-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Cross: End-Bond-Torsion¶
Functional Form¶
The End-Bond-Torsion Cross Potential has the functional form:
\(E=\left( {{R}_{jk}}-{{R}_{1,jk}} \right)\left[ {{B}_{1,ijkl}}\cos \left( {{\phi }_{ijkl}} \right)+{{B}_{2,ijkl}}\cos \left( 2{{\phi }_{ijkl}} \right)+{{B}_{3,ijkl}}\cos \left( 3{{\phi }_{ijkl}} \right) \right]\) \(\qquad +\left( {{R}_{kl}}-{{R}_{3,kl}} \right)\left[ {{C}_{1,ijkl}}\cos \left( {{\phi }_{ijkl}} \right)+{{C}_{2,ijkl}}\cos \left( 2{{\phi }_{ijkl}} \right)+{{C}_{3,ijkl}}\cos \left( 3{{\phi }_{ijkl}} \right) \right]\)
This term is part of the Class2 Dihedral Potential style.
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(B_{1,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/length |
| \(B_{2,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/length |
| \(B_{3,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/length |
| \(C_{1,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/length |
| \(C_{2,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/length |
| \(C_{3,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/length |
| \(R_{1,jk}\) | Equilibrium bond length for atoms [i,j] | length |
| \(R_{3,kl}\) | Equilibrium bond length for atoms [k,l] | length |
XML Schema¶
The XML schema for the End-Bond-Torsion Cross Potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Cosine term coefficient for atoms [i,j,k,l] | \(B_{1,ijkl}\) | B1 |
| Cosine term coefficient for atoms [i,j,k,l] | \(B_{2,ijkl}\) | B2 |
| Cosine term coefficient for atoms [i,j,k,l] | \(B_{3,ijkl}\) | B3 |
| Cosine term coefficient for atoms [i,j,k,l] | \(C_{1,ijkl}\) | C1 |
| Cosine term coefficient for atoms [i,j,k,l] | \(C_{2,ijkl}\) | C2 |
| Cosine term coefficient for atoms [i,j,k,l] | \(C_{3,ijkl}\) | C3 |
| Equilibrium bond length for atoms [i,j] | \(R_{1,ij}\) | R1 |
| Equilibrium bond length for atoms [k,l] | \(R_{3,kl}\) | R3 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | EndBondTorsion |
| formula | Fixed | (R-R1)*[B1*cos(Phi)+B2*cos(2*Phi)+B3*cos(3*Phi)]+(R-R3)*[C1*cos(Phi)+C2*cos(2*Phi)+C3*cos(3*Phi)] |
| B-units | Required | Enumerations specified in schema |
| C-units | Required | Enumerations specified in schema |
| R-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Cross: Angle-Torsion¶
Functional Form¶
The Angle-Torsion Cross Potential has the functional form:
\(E=\left( {{\theta }_{ijk}}-{{\theta }_{1,ijk}} \right)\left[ {{D}_{1,ijkl}}\cos \left( {{\phi }_{ijkl}} \right)+{{D}_{2,ijkl}}\cos \left( 2{{\phi }_{ijkl}} \right)+{{D}_{3,ijkl}}\cos \left( 3{{\phi }_{ijkl}} \right) \right]\) \(\qquad +\left( {{\theta }_{jkl}}-{{\theta }_{2,jkl}} \right)\left[ {{E}_{1,ijkl}}\cos \left( {{\phi }_{ijkl}} \right)+{{E}_{2,ijkl}}\cos \left( 2{{\phi }_{ijkl}} \right)+{{E}_{3,ijkl}}\cos \left( 3{{\phi }_{ijkl}} \right) \right]\)
This term is part of the Class2 Dihedral Potential style.
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(D_{1,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/degrees |
| \(D_{2,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/degrees |
| \(D_{3,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/degrees |
| \(E_{1,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/degrees |
| \(E_{2,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/degrees |
| \(E_{3,ijkl}\) | Cosine term coefficient for atoms [i,j,k,l] | energy/degrees |
| \({\theta}_{1,ijk}\) | Equilibrium bond length for atoms [i,j] | degrees |
| \({\theta}_{2,jkl}\) | Equilibrium bond length for atoms [k,l] | degrees |
XML Schema¶
The XML schema for the Angle-Torsion Cross Potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Cosine term coefficient for atoms [i,j,k,l] | \(D_{1,ijkl}\) | D1 |
| Cosine term coefficient for atoms [i,j,k,l] | \(D_{2,ijkl}\) | D2 |
| Cosine term coefficient for atoms [i,j,k,l] | \(D_{3,ijkl}\) | D3 |
| Cosine term coefficient for atoms [i,j,k,l] | \(E_{1,ijkl}\) | E1 |
| Cosine term coefficient for atoms [i,j,k,l] | \(E_{2,ijkl}\) | E2 |
| Cosine term coefficient for atoms [i,j,k,l] | \(E_{3,ijkl}\) | E3 |
| Equilibrium bond length for atoms [i,j] | \({\theta}_{1,ijk}\) | Theta1 |
| Equilibrium bond length for atoms [k,l] | \({\theta}_{2,jkl}\) | Theta2 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | AngleTorsion |
| formula | Fixed | (Theta-Theta1)*[D1*cos(Phi)+D2*cos(2*Phi)+D3*cos(3*Phi)]+(Theta-Theta2)*[E1*cos(Phi)+E2*cos(2*Phi)+E3*cos(3*Phi)] |
| D-units | Required | Enumerations specified in schema |
| E-units | Required | Enumerations specified in schema |
| Theta-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Cross: Angle-Angle-Torsion¶
Functional Form¶
The Angle-Angle-Torsion Cross Potential has the functional form:
\(E={{M}_{ijkl}}\left( {{\theta }_{ijk}}-{{\theta }_{1,ijk}} \right)\left( {{\theta }_{jkl}}-{{\theta }_{2,jkl}} \right)\cos \left( {{\phi }_{ijkl}} \right)\)
This term is part of the Class2 Dihedral Potential style.
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(M_{ijkl}\) | Bond coefficient for atoms [i,j,k,l] | energy |
| \({\theta}_{1,ijk}\) | Equilibrium angle for atoms [i,j,k] | degrees |
| \({\theta}_{2,jkl}\) | Equilibrium angle for atoms [j,k,l] | degrees |
XML Schema¶
The XML schema for the Angle-Angle-Torsion Cross Potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Bond coefficient for atoms [i,j,k,l] | \(M_{ijkl}\) | M |
| Equilibrium angle for atoms [i,j,k] | \({\theta}_{1,ijk}\) | Theta1 |
| Equilibrium angle for atoms [j,k,l] | \({\theta}_{2,jkl}\) | Theta2 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | AngleAngleTorsion |
| formula | Fixed | M(Theta-Theta1)*(Theta-Theta2)*cos(Phi) |
| M-units | Required | Enumerations specified in schema |
| Theta-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Non-Bond Potentials¶
Non-Bond Lennard-Jones Potential¶
Functional Form¶
The non-bond Lennard-Jones potential has the functional form:
\(E = 4 \cdot {\epsilon} \cdot \left[ {\left( \frac {\sigma}{R_{ij}} \right)^{12} - \left( \frac {\sigma}{R_{ij}} \right)^{6}} \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(\epsilon\) | Potential well depth for atom [i] | energy/mol |
| \(\sigma\) | Interatomic cut-off distance for atom [i] | length |
XML Schema¶
The XML schema for the non-bond Lennard-Jones potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AtomType |
| Potential well depth for atom [i] | \(\epsilon\) | epsilon |
| Interatomic cut-off distance for atom [i] | \(\sigma\) | sigma |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Lennard-Jones (12-6) |
| formula | Fixed | 4*epsilon*[(sigma/R)^12-(sigma/R)^6] |
| epsilon-units | Required | Enumerations specified in schema |
| sigma-units | Required | Enumerations specified in schema |
| Combining-Rule | Required | Combining rule for mixed atom types |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Non-Bond Lennard-Jones Potential¶
Functional Form¶
The non-bond Lennard-Jones potential has the functional form:
\(E = 4 \cdot {\epsilon} \cdot \left[ {\left( \frac {\sigma}{R_{ij}} \right)^{12} - \left( \frac {\sigma}{R_{ij}} \right)^{6}} \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(\epsilon\) | Potential well depth for atom [i] | energy/mol |
| \(\sigma\) | Interatomic cut-off distance for atom [i] | length |
XML Schema¶
The XML schema for the non-bond Lennard-Jones potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AT-1 |
| Atom type of atom [j] | (implicit) | AT-2 |
| Potential well depth for atom [i] | \(\epsilon\) | epsilon |
| Interatomic cut-off distance for atom [i] | \(\sigma\) | sigma |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Lennard-Jones (12-6) |
| formula | Fixed | 4*epsilon*[(sigma/R)^12-(sigma/R)^6] |
| epsilon-units | Required | Enumerations specified in schema |
| sigma-units | Required | Enumerations specified in schema |
| Combining-Rule | Required | Combining rule for mixed atom types |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Non-Bond Lennard-Jones (9-6 Form) Potential¶
Functional Form¶
The non-bond Lennard-Jones (9-6 Form) potential has the functional form:
\(E=\epsilon \left[ 2{{\left( \frac{{\sigma}}{{{R}_{ij}}} \right)}^{9}}-3{{\left( \frac{{\sigma}}{{{R}_{ij}}} \right)}^{6}} \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(\epsilon\) | Potential well depth for atom [i] | energy/mol |
| \(\sigma\) | Interatomic cut-off distance for atom [i] | length |
XML Schema¶
The XML schema for the non-bond Lennard-Jones (9-6 Form) potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AtomType |
| Potential well depth for atom [i] | \(\epsilon\) | epsilon |
| Interatomic cut-off distance for atom [i] | \(\sigma\) | sigma |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Lennard-Jones (9-6) [Class 2 Form] |
| formula | Fixed | epsilon*[2*(sigma/R)^9-3*(sigma/R)^6] |
| epsilon-units | Required | Enumerations specified in schema |
| sigma-units | Required | Enumerations specified in schema |
| Combining-Rule | Required | Combining rule for mixed atom types |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Non-Bond Lennard-Jones Potential - AB Form¶
Functional Form¶
The non-bond Lennard-Jones (AB Form) potential has the functional form:
\(E=\frac{{{A}_{ij}}}{R_{ij}^{12}}-\frac{{{B}_{ij}}}{R_{ij}^{6}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(A_{ij}\) | General 12th power Lennard-Jones coefficient [i] | energy*length^12/mol |
| \(B_{ij}\) | General 6th power Lennard-Jones coefficient [i] | energy*length^6/mol |
XML Schema¶
The XML schema for the non-bond Lennard-Jones (AB Form) potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AtomType |
| General 12th power Lennard-Jones coefficient [i] | \(A_{ij}\) | A |
| General 6th power Lennard-Jones coefficient [i] | \(B_{ij}\) | B |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Lennard-Jones (12-6) [A-B Form] |
| formula | Fixed | A/(R^12)-B/(R^6) |
| A–units | Required | Enumerations specified in schema |
| B-units | Required | Enumerations specified in schema |
| Combining-Rule | Required | Combining rule for mixed atom types |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Non-Bond Lennard-Jones Potential - AB Form (Two atom types)¶
Functional Form¶
The non-bond Lennard-Jones (AB Form) potential has the functional form:
\(E=\frac{{{A}_{ij}}}{R_{ij}^{12}}-\frac{{{B}_{ij}}}{R_{ij}^{6}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(A_{ij}\) | General 12th power Lennard-Jones coefficient [i] | energy*length^12/mol |
| \(B_{ij}\) | General 6th power Lennard-Jones coefficient [i] | energy*length^6/mol |
XML Schema¶
The XML schema for the non-bond Lennard-Jones (AB Form) potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AT-1 |
| Atom type of atom [j] | (implicit) | AT-2 |
| General 12th power Lennard-Jones coefficient [i] | \(A_{ij}\) | A |
| General 6th power Lennard-Jones coefficient [i] | \(B_{ij}\) | B |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Lennard-Jones (12-6) [A-B Form] |
| formula | Fixed | A/(R^12)-B/(R^6) |
| A–units | Required | Enumerations specified in schema |
| B-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Non-Bond Lennard-Jones (Rmin Form) Potential¶
Functional Form¶
The non-bond Lennard-Jones (Rmin Form) potential has the functional form:
\(E=\epsilon \left[ {{\left( \frac{{{R}_{\min ,ij}}}{{{R}_{ij}}} \right)}^{12}}-2{{\left( \frac{{{R}_{\min ,ij}}}{{{R}_{ij}}} \right)}^{6}} \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(\epsilon\) | Potential well depth for atom [i] | energy/mol |
| \(R_{min,ij}\) | Interatomic cut-off distance for atom [i] | length |
XML Schema¶
The XML schema for the non-bond Lennard-Jones (Rmin Form) potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AtomType |
| Potential well depth for atom [i] | \(\epsilon\) | epsilon |
| Distance at the Lennard-Jones minimum [i] | \(R_{min,ij}\) | Rmin |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Lennard-Jones (12-6) [Rmin Form] |
| formula | Fixed | epsilon*[(Rmin/R)^12-2*(Rmin/R)^6] |
| epsilon-units | Required | Enumerations specified in schema |
| Rmin-units | Required | Enumerations specified in schema |
| Combining-Rule | Required | Combining rule for mixed atom types |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Non-Bond Lennard-Jones GROMACS Potential¶
Functional Form¶
The non-bond Lennard-Jones GROMACS potential has the functional form:
\(E = 4 \cdot {\epsilon} \cdot \left[ {\left( \frac {\sigma}{R_{ij}} \right)^{12} - \left( \frac {\sigma}{R_{ij}} \right)^{6}} \right] + {S_{LJ}}\left({R_{ij}}\right)\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(\epsilon\) | Potential well depth for atom [i] | energy/mol |
| \(\sigma\) | Interatomic cut-off distance for atom [i] | length |
XML Schema¶
The XML schema for the non-bond Lennard-Jones GROMACS potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AtomType |
| Potential well depth for atom [i] | \(\epsilon\) | epsilon |
| Interatomic cut-off distance for atom [i] | \(\sigma\) | sigma |
| Inner cut-off distance for atom [i] | r_1 | |
| Outer cut-off distance for atom [i] | r_cut |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Lennard-Jones (12-6) |
| formula | Fixed | 4*epsilon*[(sigma/R)^12-(sigma/R)^6] + S_LJ(R) |
| epsilon-units | Required | Enumerations specified in schema |
| sigma-units | Required | Enumerations specified in schema |
| r-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Non-Bond Lennard-Jones (Class 2 Form) Potential¶
Functional Form¶
The non-bond Lennard-Jones (Class 2 Form) potential has the functional form:
\(E=\epsilon \left[ 2{{\left( \frac{{R_{min}}}{{{R}_{ij}}} \right)}^{9}}-3{{\left( \frac{{R_{min}}}{{{R}_{ij}}} \right)}^{6}} \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(\epsilon\) | Potential well depth for atom [i] | energy/mol |
| \(R_{min}\) | Interatomic cut-off distance for atom [i] | length |
XML Schema¶
The XML schema for the non-bond Lennard-Jones (9-6 Form) potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AtomType |
| Potential well depth for atom [i] | \(\epsilon\) | epsilon |
| Interatomic cut-off distance for atom [i] | \(\sigma\) | sigma |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Lennard-Jones (9-6) [Class 2 Form] |
| formula | Fixed | epsilon*[2*(Rmin/R)^9-3*(Rmin/R)^6] |
| epsilon-units | Required | Enumerations specified in schema |
| sigma-units | Required | Enumerations specified in schema |
| Combining-Rule | Required | Combining rule for mixed atom types |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Non-Bond Energy Renormalization Potential¶
Functional Form¶
The non-bond Energy Renormalization potential has the functional form:
\(E=\left( {{\epsilon }_{A}}-{{\epsilon }_{g}} \right)\left[ \frac{1}{1+{{e}^{-k\left( T-{{T}_{T}} \right)}}} \right]+{{\epsilon }_{g}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \({\epsilon }_{A}\) | Epsilon value in Arrhenius regime | energy/mol |
| \({\epsilon }_{g}\) | Epsilon value in glassy regime | energy/mol |
| \(k\) | Temperature breadth of the transition | N/A |
| \({T}_{T}\) | Crossover point of sigmoidal function | temperature |
XML Schema¶
The XML schema for the non-bond Energy Renormalization potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AT1 |
| Atom type of atom [j] | (implicit) | AT2 |
| Epsilon value in Arrhenius regime | \({\epsilon }_{A}\) | epsilon_A |
| Epsilon value in glassy regime | \({\epsilon }_{g}\) | epsilon_g |
| Temperature breadth of the transition | \(k\) | k_sig |
| Exponent of attractive term | \({\gamma }_{att}\) | n_att |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Mie |
| formula | Fixed | C*epsilon*[(sigma/R)^m_rep-(sigma/R)^n_att] |
| a_ij-units | Required | Enumerations specified in schema |
| r_c-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
- LAMMPS Mie Pair Potential.
- Liquid XML Studio.
- Wenjie Xia, Jake Song, Cheol Jeong, David D. Hsu, Frederick R. Phelan Jr., Jack F. Douglas, Sinan Keten, “Energy-Renormalization for Achieving Temperature Transferable Coarse-Graining of Polymer Dynamics,” Macromolecules, 50 (21), pp. 8787–8796, (2017). DOI: 10.1021/acs.macromol.7b01717
- Wenjie Xia, Jake Song, Nitin H. Krishnamurthy, Frederick R. Phelan Jr., Sinan Keten, Jack F. Douglas, “Energy Renormalization for Coarse-Graining the Dynamics of a Model Glass-Forming Liquid,” Journal of Physical Chemistry B, 122 (6), pp. 2040-2045, (2018). DOI: 10.1021/acs.jpcb.8b00321
- Jake Song, David D. Hsu, Kenneth R. Shull, Frederick R. Phelan Jr., Jack F. Douglas, Wenjie Xia, Sinan Keten, “Energy Renormalization Method for the Coarse-Graining of Polymer Viscoelasticity,” Macromolecules, 51(10), pp. 3818–3827, (2018). DOI: 10.1021/acs.macromol.7b02560
- Wenjie Xia, Nitin K. Hansoge, Wen-Sheng Xu, Frederick R. Phelan Jr., Sinan Keten, and Jack F. Douglas, “Energy renormalization for coarse-graining polymers having different segmental structures,” Science Advances 5(4), eaav4683, (19 Apr 2019). DOI: 10.1126/sciadv.aav4683
Non-Bond Mie Potential¶
Functional Form¶
The non-bond Mie potential has the functional form:
\(E=C\epsilon \left[ {{\left( \frac{{{\sigma }_{ij}}}{{{R}_{ij}}} \right)}^{{{\gamma }_{rep}}}}-{{\left( \frac{{{\sigma }_{ij}}}{{{R}_{ij}}} \right)}^{{{\gamma }_{att}}}} \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(\epsilon\) | Potential well depth for atom [i] | energy/mol |
| \(\sigma\) | Interatomic cut-off distance for atom [i] | length |
| \({\gamma }_{rep}\) | Exponent of repulsive term | N/A |
| \({\gamma }_{att}\) | Exponent of attractive term | N/A |
XML Schema¶
The XML schema for the non-bond Mie potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AT1 |
| Atom type of atom [j] | (implicit) | AT2 |
| Potential well depth for atom [i] | \(\epsilon\) | epsilon |
| Interatomic cut-off distance for atom [i] | \(\sigma\) | sigma |
| Exponent of repulsive term | \({\gamma }_{rep}\) | m_rep |
| Exponent of attractive term | \({\gamma }_{att}\) | n_att |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Mie |
| formula | Fixed | C*epsilon*[(sigma/R)^m_rep-(sigma/R)^n_att] |
| a_ij-units | Required | Enumerations specified in schema |
| r_c-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Non-Bond Soft Potential¶
Functional Form¶
The non-bond Soft potential has the functional form:
\(E={{A}_{ij}}\left[ 1+\cos \left( \frac{\pi R}{{{R}_{c}}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(A_{ij}\) | Coefficient for atom [i] | energy/mol |
| \(R_{c}\) | Interatomic cut-off distance for atom [i] | length |
XML Schema¶
The XML schema for the non-bond Soft potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AT1 |
| Atom type of atom [j] | (implicit) | AT2 |
| Coefficient for atom [i] | \(A_{ij}\) | a_ij |
| Interatomic cut-off distance for atom [i] | \(R_{c}\) | r_c |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Soft |
| formula | Fixed | a_ij*[1+cos(pi*r/r_c)] |
| a_ij-units | Required | Enumerations specified in schema |
| r_c-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Tabular Non-Bond¶
Tabular Form¶
The tabular non-bond potential has the parameters:
| Parameter | Parameter Definition | Units |
| N | Number of tabulated values | N/A |
| R | Interatomic distance (least: rlo, greatest: rhi) | length |
| RSQ | Interatomic distance squared (least: rlo, greatest: rhi) | length^2 |
| BITMAP | Determines ordering of tabulated values (least: rlo, greatest: rhi) | length |
| FPRIME | Derivatives of the force at the innermost (fplo) and outermost (fphi) bond lengths | force/length length^2 |
The tabular non-bond potential has the tabulated values:
| index | r | energy | force |
| i_1 | r_1 | e_1 | f_1 |
| … | … | … | … |
| i_N | r_N | e_n | f_N |
XML Schema¶
The XML schema for the tabular non-ond potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the parameters/symbols and XML schema notations are given by:
| Parameter Definition | Parameter/Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Section identifying keyword | N/A | keyword |
| Number of tabulated values | N | N |
| Interatomic distance (least) | R | rlo |
| Interatomic distance (greatest) | R | rhi |
| Interatomic distance squared (least) | RSQ | rlo |
| Interatomic distance squared (greatest) | RSQ | rhi |
| Determines ordering of tabulated values (least) | BITMAP | rlo |
| Determines ordering of tabulated values (greatest) | BITMAP | rhi |
| Derivative of the force at the innermost | FPRIME | fplo |
| Derivative of the force at the outermost | FPRIME | fphi |
| Index | index | index |
| Interatomic distance | r | r |
| Energy | energy | energy |
| Force | force | force |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Tabular |
| Interpolation-style | Required | Enumerations specified in schema |
| r-units | Required | Enumerations specified in schema |
| energy-units | Required | Enumerations specified in schema |
| force-units | Required | Enumerations specified in schema |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Non-Bond Weeks-Chandler-Anderson Potential¶
Functional Form¶
The non-bond Weeks-Chandler-Anderson potential has the functional form:
\(E=4\epsilon \left[ {{\left( \frac{{{\sigma }_{ij}}}{{{R}_{ij}}} \right)}^{12}}-{{\left( \frac{{{\sigma }_{ij}}}{{{R}_{ij}}} \right)}^{12}}+\frac{1}{4} \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(\epsilon\) | Potential well depth for atom [i] | energy/mol |
| \(\sigma\) | Interatomic cut-off distance for atom [i] | length |
XML Schema¶
The XML schema for the non-bond Weeks-Chandler-Anderson potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | (implicit) | AT-1 |
| Atom type of atom [j] | (implicit) | AT-2 |
| Potential well depth for atom [i] | \(\epsilon\) | epsilon |
| Interatomic cut-off distance for atom [i] | \(\sigma\) | sigma |
| Interatomic cut-off distance for atom [i] | N/A | r_cut |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Weeks-Chandler-Anderson |
| formula | Fixed | 4*epsilon*[((sigma/R)^-12)-((sigma/R)^-6)+(1/4)] |
| epsilon-units | Required | Enumerations specified in schema |
| sigma-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
Table Potentials¶
Bond Increment Table¶
The XML schema for the bond increment table has the following representation (design mode representation using Liquid XML Studio):
The specific elements (describing each set of parameters) are given by:
| Parameter Definition | Schema Notation |
| Atom type of atom [i] | AT-I |
| Atom type of atom [j] | AT-J |
| Increment step size for atoms [i,j] | Delta-IJ |
| Increment step size for atoms [j,i] | Delta-JI |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Equivalence Table¶
The XML schema for the equivalence table has the following representation (design mode representation using Liquid XML Studio):
The specific elements (describing each set of parameters) are given by:
| Parameter Definition | Schema Notation |
| Atom type of atom [i] | AtomType |
| NonBond | |
| Bond | |
| Angle | |
| Dihedral | |
| Improper |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Auto-Equivalence Table¶
The XML schema for the auto-equivalence table has the following representation (design mode representation using Liquid XML Studio):
The specific elements (describing each set of parameters) are given by:
| Parameter Definition | Schema Notation |
| Atom type of atom [i] | AtomType |
| NonBond | |
| BondIncrement | |
| Bond | |
| AngleEnd | |
| AngleApex | |
| DihedralEnd | |
| DihedralCenter | |
| OutOfPlaneEnd | |
| OutOfPlaneCenter |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Mesoscale Potentials¶
Langevin Dissipative¶
Functional Form¶
The Langevin dissipative potential has the functional form:
\(E=\gamma\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(\gamma\) | Langevin thermostat | mass/time |
XML Schema¶
The XML schema for the Langevin dissipative potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Langevin thermostat | \(\gamma\) | gamma |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | Langevin |
| formula | Fixed | gamma |
| gamma-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
DPD Soft¶
Functional Form¶
The DPD soft potential has the functional form:
\(E={{A}_{ij}}\left( 1-\frac{{{R}_{ij}}}{{{R}_{c}}} \right)-\gamma {{\left( 1-\frac{{{R}_{ij}}}{{{R}_{c}}} \right)}^{2}}+\sigma \left( 1-\frac{{{R}_{ij}}}{{{R}_{c}}} \right)\alpha {{(\Delta T)}^{-\frac{1}{2}}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(A_{ij}\) | Coefficient for conservative force | force |
| \(\gamma\) | Coefficient for dissipative force | force/velocity |
| \(R_{c}\) | Cutoff distance value | length |
XML Schema¶
The XML schema for the soft DPD potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Coefficient for conservative force | \(A_{ij}\) | a_ij |
| Coefficient for dissipative force | \(\gamma\) | gamma |
| Cutoff distance value | \(R_{c}\) | r_c |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | DPD |
| formula | Fixed | a_ij*(1-r/r_c)-gamma*(1-r/r_c)^2+sigma*(1-r/r_c)*alpha*deltaT^(-1/2) |
| a_ij-units | Required | Enumerations specified in schema |
| gamma-units | Required | Enumerations specified in schema |
| r_c-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
SRP Soft¶
Functional Form¶
The SRP soft potential has the functional form:
\(E={{C}_{ij}}\left( 1-\frac{{{R}_{ij}}}{{{R}_{c}}} \right)\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(C_{ij}\) | Coefficient for repulsive force | force |
| \(R_{c}\) | Cutoff distance value | length |
XML Schema¶
The XML schema for the soft SRP potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Coefficient for repulsive force | \(C_{ij}\) | c_ij |
| Cutoff distance value | \(R_{c}\) | r_c |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| style | Fixed | SRP |
| formula | Fixed | c_ij*(1-r/r_c) |
| c_ij-units | Required | Enumerations specified in schema |
| r_c-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Value/Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
References¶
Water Models¶
3Site-Rigid Water Model¶
Functional Form¶
The 3Site-Rigid water model has the functional form:
\(E={{E}_{q}}+{{E}_{LJ}}\)
or alternatively:
\(E={{E}_{q}}+{{E}_{LJ}}+{{E}_{pol}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(E_{q}\) | Charge potential energy | energy |
| \(E_{LJ}\) | Lennard-Jones potential energy | energy |
| \(E_{pol}\) | Average polarization correction | energy |
XML Schema¶
The XML schema for the 3Site-Rigid water model has the following representation (design mode representation using Liquid XML Studio):
The general sub-elements (the actual data set) are given by:
| Parameter Definition | Schema Notation |
| Distance between O and H | R_OH |
| Angle between HOH | Theta_HOH |
| Lennard-Jones parameter | A |
| Lennard-Jones parameter | B |
| Charge of O | q_O |
| Charge of H | q_H |
| EnergyDispersion | |
| sigma | |
| epsilon |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| name | Required | The name |
| formula | Fixed | E=E_q+E_LJ | E=E_q+E_LJ+E_pol |
| version | Optional | Version number of parameter set |
| comment | Optional | Comment attached to data set |
| R_OH-units | Required | Enumerations specified in schema |
| Theta_HOH-units | Required | Enumerations specified in schema |
| A-units | Required | Enumerations specified in schema |
| B-units | Required | Enumerations specified in schema |
| sigma-units | Required | Enumerations specified in schema |
| epsilon-units | Required | Enumerations specified in schema |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
4Site-Rigid Water Model¶
Functional Form¶
The 4Site-Rigid water model has the functional form:
\(E={{E}_{q}}+{{E}_{LJ}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(E_{q}\) | Charge potential energy | energy |
| \(E_{LJ}\) | Lennard-Jones potential energy | energy |
XML Schema¶
The XML schema for the 4Site-Rigid water model has the following representation (design mode representation using Liquid XML Studio):
The general sub-elements (the actual data set) are given by:
| Parameter Definition | Schema Notation |
| Distance between O and H | R_OH |
| Distance between O and M | R_OM |
| Angle between HOH | Theta_HOH |
| Lennard-Jones parameter | A |
| Lennard-Jones parameter | B |
| Charge of M | q_M |
| Charge of H | q_H |
| sigma | |
| epsilon |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| name | Required | The name |
| formula | Fixed | E=E_q+E_LJ |
| version | Optional | Version number of parameter set |
| comment | Optional | Comment attached to data set |
| A-units | Required | Enumerations specified in schema |
| B-units | Required | Enumerations specified in schema |
| R-units | Required | Enumerations specified in schema |
| Theta_HOH-units | Required | Enumerations specified in schema |
| sigma-units | Required | Enumerations specified in schema |
| epsilon-units | Required | Enumerations specified in schema |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.
5Site-Rigid Water Model¶
Functional Form¶
The 5Site-Rigid water model has the functional form:
\(E={{E}_{q}}+{{E}_{LJ}}\)
or alternatively:
\(E=S\left( {{R}_{ij}} \right){{E}_{q}}+{{E}_{LJ}}\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(E_{q}\) | Charge potential energy | energy |
| \(E_{LJ}\) | Lennard-Jones potential energy | energy |
| \(S\left( {{R}_{ij}} \right)\) | Switching function | N/A |
XML Schema¶
The XML schema for the 5Site-Rigid water model has the following representation (design mode representation using Liquid XML Studio):
The general sub-elements (the actual data set) are given by:
| Parameter Definition | Schema Notation |
| Distance between O and H | R_OH |
| Distance between O and M | R_OL |
| Angle between HOH | Theta_HOH |
| Angle between LOL | Theta_LOL |
| Lennard-Jones parameter | A |
| Lennard-Jones parameter | B |
| Charge of L | q_L |
| Charge of H | q_H |
| R_L | |
| R_ij | |
| sigma | |
| epsilon |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value/Definition |
| name | Required | The name |
| formula | Fixed | E=E_q+E_LJ |
| version | Optional | Version number of parameter set |
| comment | Optional | Comment attached to data set |
| A-units | Required | Enumerations specified in schema |
| B-units | Required | Enumerations specified in schema |
| R-units | Required | Enumerations specified in schema |
| Theta-units | Required | Enumerations specified in schema |
| sigma-units | Required | Enumerations specified in schema |
| epsilon-units | Required | Enumerations specified in schema |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.