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

• DOI: 10.1016/j.cpc.2018.10.006
• Publication Date: 2018-10-17T15:28:17Z
• Authors: Iain Bethune; Ralf Banisch; Elena Breitmoser; Antonia B.K. Collis; Gordon Gibb; Gianpaolo Gobbo; Charles Matthews; Graeme J. Ackland; Benedict J. Leimk...
• Keywords: 0103 physical sciences; FOS: Physical sciences; Computational Physics (physics.comp-ph); Physics - Computational Physics; 01 natural sciences

Pre-print accepted for Computer Physics Communications<br/>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.<br/>