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Integrated tools for molecular dynamics simulation data analysis in the MolDynGrid virtual laboratory

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5 Author(s)
O. V. Savytskyi ; Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Akademika Zabolotnogo Str., 150, Kyiv-03680, Ukraine ; I. A. Sliusar ; S. O. Yesylevskyy ; S. G. Stirenko
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Existing molecular modeling software and different techniques of molecular dynamics trajectories analysis were evaluated in terms of subsequent integration into the MolDynGrid virtual laboratory services. GROMACS 4 molecular dynamics package contains the most comprehensive set of analytical programs, thus the standard analytical tools in MolDynGrid were based on this software. G_correlation tool was ported to GPU which dramatically increased its productivity. Scripting capabilities of VMD software were used for certain non-standard analysis techniques, while complex and computationally intensive techniques were implemented using Pteros molecular modeling library. Parallel execution of analytical programs was implemented in MolDynGrid by a set of internally developed scripts.

Published in:

Intelligent Data Acquisition and Advanced Computing Systems (IDAACS), 2011 IEEE 6th International Conference on  (Volume:1 )

Date of Conference:

15-17 Sept. 2011