Single‐pass incremental force updates for adaptively restrained molecular dynamics. Issue 8 (11th December 2017)

• Record Type: Journal Article
• Authors: Singh, Krishna Kant; Redon, Stephane
• Is Part Of: Journal of computational chemistry. Volume 39:Issue 8(2018)
• Page Start: 412
• Page End: 423
• Publication Date: 2017-12-11
• Subjects: neighbor lists -- incremental force update -- adaptively restrained molecular dynamics; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.25126
• Languages: English
• ISSNs: 0192-8651

Abstract

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. © 2017 Wiley Periodicals, Inc. Abstract : This figure represents the configuration space explored by all‐atom molecular dynamics and adaptively restrained molecular dynamics (with different restraining parameters) simulations. Adaptively switching the positional degrees of freedom on and off not only allows to perform more number of integration steps but also produces the unbiased and equilibrium statistics of the system.