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Single-pass Incremental Force Updates for Adaptively Restrained Molecular Dynamics

Krishna Kant Singh 1 Stephane Redon 1 
1 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, Grenoble INP - Institut polytechnique de Grenoble - Grenoble Institute of Technology, LJK - Laboratoire Jean Kuntzmann
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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Submitted on : Wednesday, November 15, 2017 - 6:12:08 PM
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Krishna Kant Singh, Stephane Redon. Single-pass Incremental Force Updates for Adaptively Restrained Molecular Dynamics. Journal of Computational Chemistry, 2018, 39 (8), pp.412-423. ⟨10.1002/jcc.25126⟩. ⟨hal-01635863⟩



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