Single-pass Incremental Force Updates for Adaptively Restrained Molecular Dynamics

Krishna Singh 1 Stephane Redon 1
1 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, INPG - Institut National Polytechnique de Grenoble
Abstract : Adaptively Restrained Molecular dynamics (ARMD) allows users to perform more integration steps in wall-clock time by switching on and off positional degrees of freedoms. This article presents new, single-pass incremental force updates algorithms to efficiently simulate a system using ARMD. We assessed different algorithms for speedup measurements and implemented them in the LAMMPS MD package. We validated the single-pass incremental force update algorithm on four different benchmarks using diverse pair potentials. The proposed algorithm allows us to perform simulation of a system faster than traditional MD in both NVE and NVT ensembles. Moreover, ARMD using the new single-pass algorithm speeds up the convergence of observables in wall-clock time.
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Journal of Computational Chemistry, Wiley, 2017, 〈10.1002/jcc.25126〉
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Soumis le : mercredi 15 novembre 2017 - 18:12:08
Dernière modification le : jeudi 11 janvier 2018 - 06:22:10

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Krishna Singh, Stephane Redon. Single-pass Incremental Force Updates for Adaptively Restrained Molecular Dynamics. Journal of Computational Chemistry, Wiley, 2017, 〈10.1002/jcc.25126〉. 〈hal-01635863〉

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