Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 36, Issue 2, Pages 79-87Publisher
WILEY
DOI: 10.1002/jcc.23775
Keywords
classical molecular dynamics; force fields; parameterization; minimization algorithms
Categories
Funding
- National Science Foundation Scientific Software Innovations Institutes Program-NSF SI2-SSE [NSF1047875, NSF1148276]
- University of California [UC Lab 09-LR-06-117792]
- University of California Institute for Mexico and the United States (UC MEXUS)
- Consejo Nacional de Ciencia y Tecnologia de Mexico (CONACYT) [CN-13-554]
- CUDA fellowship
- Direct For Computer & Info Scie & Enginr
- Office of Advanced Cyberinfrastructure (OAC) [1148276] Funding Source: National Science Foundation
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The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field. (c) 2014 Wiley Periodicals, Inc.
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