Molecular Dynamics Simulations of Clathrate Hydrates on Specialised Hardware Platforms

Nicola Varini, Niall J. English and Christian R. Trott
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Nicola Varini: Irish Centre for High-End Computing, Trinity Enterprise Tower, Pearse St., Dublin 2, Ireland
Niall J. English: The SEC Strategic Research Cluster and the Centre for Synthesis and Chemical Biology, School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
Christian R. Trott: Scalable Algorithms, Sandia National Laboratories, Albuquerque, NM 87185-1322, USA

Energies, 2012, vol. 5, issue 9, 1-8

Abstract: Classical equilibrium molecular dynamics (MD) simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC) and TIP4P water models applied to simulation of methane hydrates, and also of liquid water, on a variety of specialised hardware platforms, in addition to estimation of various equilibrium properties of clathrate hydrates. The FPGA-based accelerator MD-GRAPE 3 was used to accelerate substantially the computation of non-bonded forces, while GPU-based platforms were also used in conjunction with CUDA-enabled versions of the LAMMPS MD software packages to reduce computational time dramatically. The dependence of molecular system size and scaling with number of processors was also investigated. Considering performance relative to power consumption, it is seen that GPU-based computing is quite attractive.

Keywords: hydrate; GPU; FPGA; molecular dynamics (search for similar items in EconPapers)
JEL-codes: Q Q0 Q4 Q40 Q41 Q42 Q43 Q47 Q48 Q49 (search for similar items in EconPapers)
Date: 2012
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (1)

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