Data scheme and data format for transferable force fields for molecular simulation
Abstract A generalized data scheme for transferable classical force fields used in molecular simulations, i.e. molecular dynamics and Monte Carlo simulation, is presented. The data scheme is implemented in an SQL-based data format. The data scheme and data format is machine readable, re-usable, and...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-07-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-023-02369-8 |
| _version_ | 1797769665274970112 |
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| author | Gajanan Kanagalingam Sebastian Schmitt Florian Fleckenstein Simon Stephan |
| author_facet | Gajanan Kanagalingam Sebastian Schmitt Florian Fleckenstein Simon Stephan |
| author_sort | Gajanan Kanagalingam |
| collection | DOAJ |
| description | Abstract A generalized data scheme for transferable classical force fields used in molecular simulations, i.e. molecular dynamics and Monte Carlo simulation, is presented. The data scheme is implemented in an SQL-based data format. The data scheme and data format is machine readable, re-usable, and interoperable. A transferable force field is a chemical construction plan specifying intermolecular and intramolecular interactions between different types of atoms or different chemical groups and can be used for building a model for a given component. The data scheme proposed in this work (named TUK-FFDat) formalizes digitally these chemical construction plans, i.e. transferable force fields. It can be applied to all-atom as well as united-atom transferable force fields. The general applicability of the data scheme is demonstrated for different types of force fields (TraPPE, OPLS-AA, and Potoff). Furthermore, conversion tools for translating the data scheme between .xls spread sheet format and the SQL-based data format are provided. The data format can readily be integrated in existing workflows, simulation engines, and force field databases as well as for linking such. |
| first_indexed | 2024-03-12T21:12:17Z |
| format | Article |
| id | doaj.art-bf5003e9a5ad4cf491d799370578e3b8 |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-03-12T21:12:17Z |
| publishDate | 2023-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj.art-bf5003e9a5ad4cf491d799370578e3b82023-07-30T11:07:07ZengNature PortfolioScientific Data2052-44632023-07-0110111710.1038/s41597-023-02369-8Data scheme and data format for transferable force fields for molecular simulationGajanan Kanagalingam0Sebastian Schmitt1Florian Fleckenstein2Simon Stephan3Laboratory of Engineering Thermodynamics (LTD), RPTU KaiserslauternLaboratory of Engineering Thermodynamics (LTD), RPTU KaiserslauternLaboratory of Engineering Thermodynamics (LTD), RPTU KaiserslauternLaboratory of Engineering Thermodynamics (LTD), RPTU KaiserslauternAbstract A generalized data scheme for transferable classical force fields used in molecular simulations, i.e. molecular dynamics and Monte Carlo simulation, is presented. The data scheme is implemented in an SQL-based data format. The data scheme and data format is machine readable, re-usable, and interoperable. A transferable force field is a chemical construction plan specifying intermolecular and intramolecular interactions between different types of atoms or different chemical groups and can be used for building a model for a given component. The data scheme proposed in this work (named TUK-FFDat) formalizes digitally these chemical construction plans, i.e. transferable force fields. It can be applied to all-atom as well as united-atom transferable force fields. The general applicability of the data scheme is demonstrated for different types of force fields (TraPPE, OPLS-AA, and Potoff). Furthermore, conversion tools for translating the data scheme between .xls spread sheet format and the SQL-based data format are provided. The data format can readily be integrated in existing workflows, simulation engines, and force field databases as well as for linking such.https://doi.org/10.1038/s41597-023-02369-8 |
| spellingShingle | Gajanan Kanagalingam Sebastian Schmitt Florian Fleckenstein Simon Stephan Data scheme and data format for transferable force fields for molecular simulation Scientific Data |
| title | Data scheme and data format for transferable force fields for molecular simulation |
| title_full | Data scheme and data format for transferable force fields for molecular simulation |
| title_fullStr | Data scheme and data format for transferable force fields for molecular simulation |
| title_full_unstemmed | Data scheme and data format for transferable force fields for molecular simulation |
| title_short | Data scheme and data format for transferable force fields for molecular simulation |
| title_sort | data scheme and data format for transferable force fields for molecular simulation |
| url | https://doi.org/10.1038/s41597-023-02369-8 |
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