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

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

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...

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Bibliographische Detailangaben
Hauptverfasser: Savytskyi, O. V., Sliusar, I. A., Yesylevskyy, S. O., Stirenko, S. G., Kornelyuk, A. I.
Format: Tagungsbericht
Sprache:eng
Schlagworte:
Analytical models
Biological system modeling
Computational modeling
CUDA
GPU
Graphics processing unit
grid
GROMACS
Laboratories
MolDynGrid
molecular dynamics
Proteins
Pteros
Trajectory
web-portal
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Beschreibung
Zusammenfassung: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.
DOI:10.1109/IDAACS.2011.6072742