Parallel molecular dynamics simulation for protein sequences on PC- cluster and server

M Butu and A Butu, JOURNAL OF OPTOELECTRONICS AND ADVANCED MATERIALS, 12, 2296-2300 (2010).

In order to reduce the time of simulation of molecular dynamics production, and to increase the system size, the simulation techniques have been developed to distribute a simulation over a set of processors. For protein sequences simulation, parallel molecular dynamics simulations have been widely used as an important basic technique. Studying molecular dynamics of protein sequences is accomplished by getting "in silico" simulation of the dynamics trajectories. Shortening the time required to obtain these trajectories is possible with parallel computing. The aim of these experiments was to analyze the optimal hardware resources needed for parallel molecular dynamics simulation method of protein sequences. For molecular dynamics simulations there were used two protein sequences - a protein having 127 aminoacids and a peptide having 9 aminoacids, CHARMM software package, PC-cluster and server.

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