MIST: A simple and efficient molecular dynamics abstraction library for integrator development
| Main Author: | Ballantyne, John |
|---|---|
| Other Authors: | Bethune, Iain, Banisch, Ralf, Breitmoser, Elena, Collis, Antonia B. K., Gibb, Gordon, Gobbo, Gianpaolo, Matthews, Charles, Ackland, Graeme J., Leimkuhler, Benedict J. |
| Format: | Dataset |
| Terbitan: |
Mendeley
, 2018
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| Subjects: | |
| Online Access: |
https:/data.mendeley.com/datasets/m2v3483r35 |
Daftar Isi:
- 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.