Gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.

ABSTRACT: Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line syntax, so that all GROMACS commands are fully available. Gmxapi has been officially supported since the GROMACS 2019 release and is enabled by default in current versions of the software. Here we describe gmxapi 0.3 and later. Beyond simply wrapping GROMACS library operations, the API permits several advanced operations that are not feasible using the prior command-line interface. First, the API allows custom user plugin code within the molecular dynamics force calculations, so users can execute custo

SUBMITTER: Irrgang ME 

PROVIDER: S-EPMC8880871 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature