Performance analysis of parallel molecular dynamics simulation for biomolecular systems

A Butu, JOURNAL OF OPTOELECTRONICS AND ADVANCED MATERIALS, 7, 3101-3106 (2005).

Although the functional dynamics of the biomolecules goes from pico to miliseconds, the time needed to compute the molecular dynamics trajectory is much longer. One method to shorten this time is the parallel simulation. This method follows from the Amdahl's Law which is governing the parallel processing. This way, there were realized a series of molecular dynamics parallel simulation experiments on two biomolecular systems. The first system has 16993 atoms and is composed by one protein with 130 amino acid residues (2021 atoms) solvated in a water box. The length of one side of the water box is 57 A. The second system has 8933 atoms and is made up by one peptide with 9 amino acid residues (140 atoms) solvated in a water box having the side length 46 A. The aim of these experiments was to set the number of PCs in a cluster for which the ratio time simulation /number of PCs in cluster is optimal.

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