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

M Eric Irrgang, Caroline Davis and Peter M Kasson

PLOS Computational Biology, 2022, vol. 18, issue 2, 1-12

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 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.Author summary: The gmxapi software provides a Python interface for molecular dynamics simulations in GROMACS. In addition to simply wrapping GROMACS commands, it supports custom user plugin code, ensemble simulation, and data-flow chaining of commands. As such, gmxapi enables the writing and execution of high-level simulation algorithms. The software ships with GROMACS and is freely available under an LGPL2 license.

Date: 2022
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1009835

DOI: 10.1371/journal.pcbi.1009835

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