gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulation
Published in Bioinformatics, 2018
Recommended citation: M Eric Irrgang, Jennifer M Hays, Peter M Kasson, gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations, Bioinformatics, Volume 34, Issue 22, 15 November 2018, Pages 3945–3947. https://doi.org/10.1093/bioinformatics/bty484
Molecular dynamics simulations have found use in a wide variety of biomolecular applications, from protein folding kinetics to computational drug design to refinement of molecular structures. Two areas where users and developers frequently need to extend the built-in capabilities of most software packages are implementing custom interactions, for instance biases derived from experimental data, and running ensembles of simulations. We present a Python high-level interface for the popular simulation package GROMACS that i) allows custom potential functions without modifying the simulation package code, ii) maintains the optimized performance of GROMACS and iii) presents an abstract interface to building and executing computational graphs that allows transparent low-level optimization of data flow and task placement. Minimal dependencies make this integrated API for the GROMACS simulation engine simple, portable and maintainable. We demonstrate this API for experimentally-driven refinement of protein conformational ensembles.