charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS

Abstract

CHARMM is one of the most widely used biomolecular force fields. Although developed in close connection with a dedicated molecular simulation engine of the same name, it is also usable with other codes. GROMACS is a well-established, highly optimized, and multipurpose software for molecular dynamics, versatile enough to accommodate many different force field potential functions and the associated algorithms. Due to conceptional differences related to software design and the large amount of numeric data inherent to residue topologies and parameter sets, conversion from one software format to another is not straightforward. Here, we present an automated and validated means to port the CHARMM force field to a format read by the GROMACS engine, harmonizing the different capabilities of the two codes in a self-documenting and reproducible way with a bare minimum of user interaction required. Being based entirely on the upstream data files, the presented approach does not involve any hard-coded data, in contrast with previous attempts to solve the same problem. The heuristic approach used for perceiving the local internal geometry is directly applicable for analogous transformations of other force fields.