Physics

Pure mathematics

Mathematics

Torsion (gastropod)

Operating system

Algorithm

Statistical physics

Force field (fiction)

Surgery

Artificial intelligence

Set (abstract data type)

Programming language

Geometry

Software

Computer science

Molecular dynamics

Simplex

Quantum mechanics

Field (mathematics)

Process (computing)

Computational science

Medicine

Quantum

Journal of Computational Chemistry

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. © 2014 Wiley Periodicals, Inc.

Paramfit: Automated optimization of force field parameters for molecular dynamics simulations