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

Published: 9 November 2018| Version 1 | DOI: 10.17632/m2v3483r35.1
Iain Bethune,
Ralf Banisch,
Elena Breitmoser,
Antonia B. K. Collis,
Gordon Gibb,
Gianpaolo Gobbo,
Charles Matthews,
Graeme J. Ackland,
Benedict J. Leimkuhler


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.



Computational Physics