drMD: Molecular Dynamics for Experimentalists

Abstract

Abstract Molecular dynamics (MD) simulations can be used by protein scientists to investigate a wide array of biologically relevant properties such as the effects of mutations on a protein’s structure and activity, or probing intermolecular interactions with small molecule substrates or other macromolecules. Within the world of computational structural biology, several programs have become popular for running these simulations, but each of these programs requires a significant time investment from the researcher to run even simple simulations. Even after learning how to run and analyse simulations, many elements remain a “black box.” This greatly limits the accessibility of molecular dynamics simulations for non-experts. Here we present drMD, an automated pipeline for running molecular dynamics simulations using the OpenMM molecular mechanics toolkit. We have created drMD with non-experts in computational biology in mind. The drMD codebase has several functions that automatically handle routine procedures associated with running molecular dynamics simulations. This greatly reduces the expertise required to run MD simulations. We have also introduced a series of quality-of-life features to make the process of running MD simulations both easier and more pleasant. Finally, drMD explains the steps it is taking interactively and, where useful, provides relevant references so the user can learn more. All these features make drMD an effective tool for learning molecular dynamics while running publication-quality simulations. drMD is open source and can be found on GitHub: https://github.com/wells-wood-research/drMD .