MIST: A simple and efficient molecular dynamics abstraction library for integrator development

Abstract

We present MIST, the Molecular Integration Simulation Toolkit, a lightweight and efficient software library written in C++ which provides an abstract interface to common molecular dynamics codes, enabling rapid and portable development of new integration schemes for molecular dynamics. The initial release provides plug-in interfaces to NAMD-Lite, GROMACS and Amber, and includes several standard integration schemes, a constraint solver, temperature control using Langevin Dynamics, and two tempering schemes. We describe the architecture and functionality of the library and the C and Fortran APIs which can be used to interface additional MD codes to MIST.We show, for a range of test systems, that MIST introduces negligible overheads for serial, shared-memory parallel, and GPU-accelerated cases, except for Amber where the native integrators run directly on the GPU itself. As a demonstration of the capabilities of MIST, we describe a simulated tempering simulation used to study the free energy landscape of Alanine-12 in both vacuum and detailed solvent conditions.Program Title: MIST — Molecular Integration Simulation ToolkitProgram Files doi:http://dx.doi.org/10.17632/m2v3483r35.1Licensing provisions: BSD 2-clauseProgramming language: C++ (C and Fortran interfaces)Nature of problem: Production Molecular Dynamics codes have become increasingly complex, making it difficult to implement new functionality, especially algorithms that modify the core MD integration loop. This places a barrier in the way of new algorithms making their way from theory to implementation.Solution method: MIST provides a simplified abstract interface for integrator developers that may be interfaced via source-code patches and a library API to a variety of MD codes, with minimal loss of performance.Restrictions and unusual features: MIST interfaces only to specific versions of MD codes: Amber 14, Gromacs 5.0.2 and NAMD-Lite 2.0.3Additional comments: MIST is freely available from https://bitbucket.org/extasy-project/mist.