gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations

Molecular dynamics simulations have found use in a wide variety of biomolecular applications, from protein folding kinetics to computational drug design to hybrid refinement of molecular structures. Two areas where users and developers frequently need to extend the built-in capabilities of most software packages are to implement custom interactions, for instance biases derived from experimental data, and to run ensembles of simulations on arbitrary computational resources. We present a Python high-level interface for the popular simulation package GROMACS that permits these capabilities in a way that 1) allows users to apply custom potential functions without modifying the simulation package code, 2) maintains the optimized per-simulation performance of GROMACS while doing so, and 3) 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 to use, portable, and maintainable. We demonstrate the utility of this API for experimentally-driven refinement of protein conformational ensembles.