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.
@article{arxiv.1805.07117,
title = {MIST: A Simple and Efficient Molecular Dynamics Abstraction Library for Integrator Development},
author = {Iain Bethune and Ralf Banisch and Elena Breitmoser and Antonia B K Collis and Gordon Gibb and Gianpaolo Gobbo and Charles Matthews and Graeme J Ackland and Benedict J Leimkuhler},
journal= {arXiv preprint arXiv:1805.07117},
year = {2018}
}
Comments
Pre-print accepted for Computer Physics Communications