Molecular Dynamics Simulations of Clathrate Hydrates on Specialised Hardware Platforms

Energies

Nicola Varini¹  Niall J. English² 

[1] Irish Centre for High-End Computing, Trinity Enterprise Tower, Pearse St., Dublin 2, Ireland; E-Mail:;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

关键词: hydrate;    GPU;    FPGA;    molecular dynamics;   

DOI  :  10.3390/en5093526

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2012 by the authors; licensee MDPI, Basel, Switzerland.