Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit

Content Provider	Semantic Scholar
Author	Myung, Hun Joo Sakamaki, Ryuji Oh, Kwang Jin Narumi, Tetsu Yasuoka, Kenji Lee, Sik
Copyright Year	2010
Abstract	We have developed CUDA-enabled version of a general purpose molecular dynamics simulation code for GPU. Implementation details including parallelization scheme and performance optimization are described. Here we have focused on the non-bonded force calculation because it is most time consuming part in molecular dynamics simulation. Timing results using CUDA-enabled and CPU versions were obtained and compared for a biomolecular system containing 23558 atoms. CUDA-enabled versions were found to be faster than CPU version. This suggests that GPU could be a useful hardware for molecular dynamics simulation.
File Format	PDF HTM / HTML
Alternate Webpage(s)	https://www.researchgate.net/profile/Kwang_Jin_Oh/publication/260562881_Accelerating_Molecular_Dynamics_Simulation_Accelerating_Molecular_Dynamics_Simulation_Using_Graphics_Processing_Unit/links/00b49531974fc01e8e000000.pdf
Language	English
Access Restriction	Open
Subject Keyword	CPU (central processing unit of computer system) CUDA Central processing unit Graphics processing unit Mathematical optimization Molecular dynamics Parallel computing Performance tuning Simulation Version
Content Type	Text
Resource Type	Article