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Publication

Title:Molecular Dynamics Simulations of Clathrate Hydrates on Specialised Hardware Platforms
Authors:Nicola Varini, Niall J English and Christian R Trott, 2012
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.
ICHEC Project:Effects of Electromagnetic Fields on Proteins
Publication:Energies 2012, 5(9), 3526-3533; doi:10.3390/en5093526
URL: http://www.mdpi.com/1996-1073/5/9/3526
Keywords: hydrate, GPU, FPGA, molecular dynamics
Status: Published

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