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New functionality is added to the LAMMPS molecular simulation package, which increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the “type label” framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools, such as VMD and OVITO. An introductory primer on the forms and use of bonded force fields is provided to motivate this new functionality and serve as an entry point for LAMMPS and OpenKIM users unfamiliar with bonded force fields. The type label framework has the potential to streamline modeling workflows that use LAMMPS by increasing the portability of software, files, and scripts for preprocessing, running, and postprocessing a molecular simulation.
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High-Order Ab Initio Valence Force Field with Chemical Pattern-Based Parameter Assignment
Bonded interactions are fundamental ingredients of molecular mechanics force fields because they directly determine the local structure of a molecule. In this work, we parametrize the advanced bonded energy functionals that consider the vibrational anharmonicity, the coupling effects, and the out-of-plane bending for sp2-hybridized atoms. It is expected that these models can describe the spectroscopic properties and overall structures of a molecule more accurately when they are used with polarizable AMOEBA-based force fields.
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- Award ID(s):
- 1856173
- PAR ID:
- 10327042
- Date Published:
- Journal Name:
- Journal of Computational Biophysics and Chemistry
- Volume:
- 21
- Issue:
- 04
- ISSN:
- 2737-4165
- Page Range / eLocation ID:
- 431 to 447
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1142/S2737416521420047
