Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field

Abstract

Coarse-grained molecular dynamics simulations of bio- and macromolecular systems offer a method of accessing otherwise unobtainable time and length scales, compared to atomistic simulation techniques. However, a limiting step is often the generation and validation of the coarse-grained models. Here, we describe a new software package, Fast-Forward, which aids parametrization of models for the widely used Martini coarse-grained force field. In comparison to other similar packages, Fast-Forward offers a system-agnostic suite of tools to parametrize molecules of any size, existing in any environment. It achieves this while maintaining ease of use and the use of interoperable file formats from the Martini software ecosystem. Through its three subprograms, the package offers tools for trajectory mapping, parameter generation, and model validation. We demonstrate the potential of the package for several different use cases, from small biological molecules (glutathione and glutathione disulfide) to models of synthetic polymers (poly(methyl methacrylate), PMMA).