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

Published: 9 Nov 2018 | Version 1 | DOI: 10.17632/m2v3483r35.1
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Description of this data

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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This data is associated with the following publication:

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

Published in: Computer Physics Communications

Latest version

  • Version 1

    2018-11-09

    Published: 2018-11-09

    DOI: 10.17632/m2v3483r35.1

    Cite this dataset

    Bethune, Iain; Banisch, Ralf; Breitmoser, Elena; Collis, Antonia B. K.; Gibb, Gordon; Gobbo, Gianpaolo; Matthews, Charles; Ackland, Graeme J.; Leimkuhler, Benedict J. (2018), “MIST: A simple and efficient molecular dynamics abstraction library for integrator development”, Mendeley Data, v1 http://dx.doi.org/10.17632/m2v3483r35.1

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The files associated with this dataset are licensed under a BSD 2-Clause ("Simplified") License licence.

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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

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