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

Iain Bethune, Ralf Banisch, Elena Breitmoser, Antonia Collis, Gordon Gibb, Gianpaolo Gobbo, Charles Matthews, Graeme Ackland, Benedict Leimkuhler

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.
Original languageEnglish
JournalComputer Physics Communications
Publication statusPublished - 17 Oct 2018


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