Parallel Adaptively Restrained Molecular Dynamics

KK Singh and DF Marin and S Redon, 2017 INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING & SIMULATION (HPCS), 308-314 (2017).

DOI: 10.1109/HPCS.2017.55

Force computations are one of the most time consuming part in performing Molecular Dynamics (MD) simulations. Adaptively Restrained Molecular Dynamics (ARMD) makes it possible to perform fewer force calculations by adaptively restraining particles positions. This paper introduces parallel algorithms for single-pass incremental force computations to take advantage of adaptive restraints using the Message Passage Interface (MPI) standard. The proposed algorithms are implemented and validated in LAMMPS, however, these algorithms can be applied to other MD simulators. We compared our algorithms with LAMMPS for performance and scalability measurements.

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