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

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

Description

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.

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Computational Physics

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