1. Single‐pass incremental force updates for adaptively restrained molecular dynamics.
- Author
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Singh, Krishna Kant and Redon, Stephane
- Subjects
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MOLECULAR dynamics , *DEGREES of freedom , *ALGORITHMS , *SIMULATION methods & models , *CLUSTER analysis (Statistics) - 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 FROM AUTHOR]- Published
- 2018
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