MIST: A Simple and Efficient Molecular Dynamics Abstraction Library for Integrator Development

Iain Bethune; Ralf Banisch; Elena Breitmoser; Antonia B K Collis; Gordon Gibb; Gianpaolo Gobbo; Charles Matthews; Graeme J Ackland; Benedict J Leimkuhler

doi:10.1016/j.cpc.2018.10.006

arXiv · 1805.07117

MIST: A Simple and Efficient Molecular Dynamics Abstraction Library for Integrator Development

Iain Bethune·Ralf Banisch·Elena Breitmoser·Antonia B K Collis·Gordon Gibb·Gianpaolo Gobbo·Charles Matthews·Graeme J Ackland·Benedict J Leimkuhler

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Abstract

We present MIST, the Molecular Integration Simulation Toolkit, a lightweight and efficient software library written in C++ which provides an abstract in- terface 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, tem- perature control using Langevin Dynamics, and two tempering schemes. We describe the architecture and functionality of the library and the C and For- tran 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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Iain Bethune, Ralf Banisch, Elena Breitmoser, Antonia B K Collis, Gordon Gibb, Gianpaolo Gobbo, Charles Matthews, Graeme J Ackland, Benedict J Leimkuhler. 2018-05-18. MIST: A Simple and Efficient Molecular Dynamics Abstraction Library for Integrator Development. https://doi.org/10.1016/j.cpc.2018.10.006

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