Speaker
Dr
Hrachya ASTSATRYAN
(Head of HPC Laboratory, Institute for Informatics and Automation Problems of the National Academy of Sciences of Armenia)
Description
The parallel molecular dynamics simulation of complex micellar system consisting of long hydrocarbon chain surfactant was carried out. The GROMACS software package, which is designed for high-performance simulation of large complex system, was applied. The simulations were paralell on Bulgarian BlueGene/P supermachine. The goal of this paper is the detail analysis of surfactant molecules in complex system. The initially random distributed surfactant molecules in aqueous solute hydration have been simulated using GROMOS united atom force field. The computation was carried out on BlueGene/P supermachine using from 256 to 1024 processors. The estimated benchmarks show about 0.5ns per day optimized by 512 processors. It should be noted that the further increase of processors (for instance, 1024 processors) do not lead to significant increase in benchmarking value and therefore 512 processors were chosen for final run. The received data shows that the long hydrocarbon chain surfactant self-assemble into small oligomers since 50ns of simulation run, meanwhile in our previous study with surfactant rich content shows that 43ns is enough for self-assembling of spherical micelle. It is planning to continue the simulation to see the self-assembling process of huge complex systems.
Primary authors
Dr
Armen Poghosyan
(Head of Bioinformatics Goup, International Scientific Educational Center, National Academy of Sciences of the Republic of Armenia)
Dr
Arsen Levonyan
(Researcher, International Scientific Educational Center, National Academy of Sciences of the Republic of Armenia)
Dr
Hrachya ASTSATRYAN
(Head of HPC Laboratory, Institute for Informatics and Automation Problems of the National Academy of Sciences of Armenia)
