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@proceedings{846560,
author = {Štěpán, Jakub and Kulhánek, Petr and Koča, Jaroslav and Mishra, Navnit Kumar},
keywords = {parallel analysis; molecular dynamics analysis; MMPB/SA},
language = {eng},
title = {Implementation of Parallel Analyzes of Molecular Dynamics Simulation Trajectories},
year = {2009}
}
TY - CONF
ID - 846560
AU - Štěpán, Jakub - Kulhánek, Petr - Koča, Jaroslav - Mishra, Navnit Kumar
PY - 2009
TI - Implementation of Parallel Analyzes of Molecular Dynamics Simulation Trajectories
KW - parallel analysis
KW - molecular dynamics analysis
KW - MMPB/SA
N2 - Molecular dynamics is widely used method of computational chemistry. With growing size of simulated systems and length of simulations, sequential analyzes of resulting trajectories become time demanding. Thus there is a need to speed up trajectory analyzes. Recently, we have designed, implemented and tested tools for fast analyzes of long molecular simulation trajectories. Our implementation uses parallel processing of trajectories with arbitrary number of processors focused on binding free energy calculations. Moreover this approach can be easily extended to other analyzes, e.g. radius of gyration, solute/solvent contacts, etc. Developed tools were applied on the calculation of binding free energies using MM/PBSA method. Two test cases were selected: a) LgtC galactosyltransferase from Niesseria meningitidis and b) lectin PA-IIL from Pseudomonas aeruginosa complexed. The 28-times acceleration on 32 processors was achieved, which shows 90 % parallel efficiency proving suitability of used approach.
ER -
ŠTĚPÁN, Jakub, Petr KULHÁNEK, Jaroslav KOČA a Navnit Kumar MISHRA. \textit{Implementation of Parallel Analyzes of Molecular Dynamics Simulation Trajectories}. 2009.
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