Adaptively Restrained Molecular Dynamics in LAMMPS

Krishna Kant 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) is a recently introduced particles simulation method that switches positional degrees of freedom on and off during simulation in order to speed up calculations. In the NVE ensemble, ARMD allows users to trade between precision and speed while, in the NVT ensemble, it makes it possible to compute statistical averages faster. Despite the conceptual simplicity of the approach, however, integrating it in existing molecular dynamics packages is non-trivial, in particular since implemented potentials should a priori be rewritten to take advantage of frozen particles and achieve a speed-up. In this paper, we present novel algorithms for integrating ARMD in LAMMPS, a popular multipurpose molecular simulation package. In particular, we demonstrate how to enable ARMD in LAMMPS without having to re-implement all available force fields. The proposed algorithms are assessed on four different benchmarks, and show how they allow us to speed up simulations up to one order of magnitude.
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Submitted on : Friday, May 19, 2017 - 4:47:38 PM
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Krishna Kant Singh, Stephane Redon. Adaptively Restrained Molecular Dynamics in LAMMPS. Modelling and Simulation in Materials Science and Engineering, IOP Publishing, 2017, 25 (5), pp.055013. ⟨10.1088/1361-651X/aa7345⟩. ⟨hal-01525253⟩



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