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

• Published in: PLoS computational biology Vol. 18; no. 2; p. e1009835
• Main Authors: Irrgang, M. Eric, Davis, Caroline, Kasson, Peter M.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.02.2022; Public Library of Science (PLoS)
• Subjects: Algorithms; Analysis; Arrays; Biology and Life Sciences; C plus plus; Computer and Information Sciences; Computer interfaces; Design; Engineering and Technology; Engines; Flow simulation; Interfaces; Libraries; Line interfaces; Logic; Medicine and Health Sciences; Methods; Molecular dynamics; Molecular Dynamics Simulation; Packaging; Physical Sciences; Python; Research and Analysis Methods; Simulation; Social Sciences; Software; United States; Sweden
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1009835

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 custom algorithms without modifying the GROMACS source. Second, the Python interface allows tasks to be dynamically defined, so high-level algorithms for molecular dynamics simulation and analysis can be coordinated with loop and conditional operations. Gmxapi makes GROMACS more accessible to custom Python scripting while also providing support for high-level data-flow simulation algorithms that were previously feasible only in external packages.