MDSCS

From HP-SEE Wiki

Latest revision as of 17:59, 6 January 2013

General Information

• Application's name: Molecular Dynamics Study of Complex Systems (MDSCS)
• Virtual Research Community: Life Sciences
• Scientific contact: Dr. Armen Poghosyan, sicnas@sci.am
• Technical contact: Dr. Hrachya Astsatryan, hrach@sci.am
• Developers: National Academy of Sciences of the Republic of Armenia
• Web site: Bioinformatics Group

Short Description

The parallel molecular dynamics simulation of complex system consisting of surfactant/polymer mixtures is planning to carry out. The self –assembling of surfactant systems is also planning to study. The molecular dynamics results together with experimental finding will help to understand the mechanism of interactions in physical point of view and, which is most important, will give us an important information concerning the conformation and localization of system components (polymer, surfactant, water, ect.). The main research method is the molecular dynamics simulation, as well as for comparison the GPS measurement and X-ray methods are planning to use. The application based on NAMD and GROMACS packages, which are designed for high-performance simulation of large molecular systems.

Problems Solved

The 50ns molecular dynamics simulation run of SDS/water/oil system in presence of polyampholyte at pH=9 have been done. It is planned to continue the additional 50ns simulation run of mentioned system at pH=4. The analysis of molecular dynamics data is done for the system at pH=9. The self-organization of surfactant/water system is in progress (currently at ~16ns run point)

Scientific and Social Impact

The investigations will help to understand the mechanism of interaction of anionic SDS and cationic/anionic/noncharged polymer and to receive important information on the dynamical and structural features of mentioned systems. The results of the proposed investigations will make an important contribution to basic researches in Colloid Physics.

Collaborations

• Institut für Chemie of Universität Potsdam, Potsdam, Germany
• International Center for Theoretical Physics, Trieste, Italy

Beneficiaries

• Main beneficiaries are research groups investigating complex systems of molecular dynamics consisting of surfactant/polymer mixtures and micelles

Number of users

20

Development Plan

• Concept: Done before the project started
• Start of alpha stage: Done before the project started
• Start of beta stage: M1-M3
• Start of testing stage: M3-M6
• Start of deployment stage: M6-M10
• Start of production stage: M11-M24

Resource Requirements

• Number of cores required for a single run: 64-2048
• Minimum RAM/core required: 4GB
• Storage space during a single run: 0.5TB
• Long-term data storage: 5TB
• Total core hours required: more than 2 000 000

Technical Features and HP-SEE Implementation

• Primary programming language: C/C++
• Parallel programming paradigm: MPI/OpenMP
• Main parallel code: NAMD, GROMACS
• Pre/post processing code: VMD package
• Application tools and libraries: NAMD, GROMACS, FFTW

Usage Example

job_script using Grid (JDL), Grid Site (PBS) or BlueGeneP

Infrastructure Usage

• Home system: ArmGrid
  • Applied for access on: 07.2011
  • Access granted on: 07.2011
  • Achieved scalability: 256 cores
• Accessed production systems: BG/BG
  • Applied for access on: 07.2011
  • Access granted on: 07.2011
  • Achieved scalability: 2048 cores

Running on Several HP-SEE Centres

• Benchmarking activities and results: The benchmarking of mentioned system was done using 512,1024,2048 and 4096 processors on BlueGene/P, Bulgaria.

Achieved Results

• Molecular Dynamics simulation run of SDS/water/oil system in presence of polyampholyte at pH=9

• Sodium dodecyl sulfate (SDS)/water system at 45ns checkpoint

Publications

• Armen H. Poghosyan, Levon H. Arsenyan, Aram A. Shahinyan, Molecular Dynamics Study of Intermediate Phase of Long Chain Alkyl Sulfonate/Water Systems, Langmuir Journal, American Chemical Society, DOI: 10.1021/la302378r
• A. Poghosyan, L. Arsenyan, H. Astsatryan, M. Gyurjyan, H. Keropyan and A. Shahinyan, Package Benchmarking on the Base of Armenian Grid Infrastructure, Journal of Communications and Network, Scientific Research Publishing, Vol. 4 No. 1, 2012, pp. 34-40, doi:10.4236/cn.2012.41005
• A. Shahinyan, P. Hakobyan, L. Arsenyan, A. Poghosyan, The study of lyotropic liquid crystal structure using the molecular dynamics method, Journal of Molecular Crystals and Liquid Crystals, 2012, DOI:10.1080/15421406.2012.687174
• A.H. Poghosyan, L. H. Arsenyan, H.V. Astsatryan, NAMD Benchmarking of Complex System on Bulgarian BlueGene/P, IEEE Proceedings of MIPRO 2012 - Jubilee 35th International Convention, Opatija, Croatia, pp. 319-321.
• A.A.Shahinyan, L.H.Arsenyan, A.H.Poghosyan, The Study of Phase Diagram of the Surfactant/Water System by Molecular Dynamics Simulation, Book of Abstracts of 5th Japan – Russia International Workshop "Molecular Simulation Studies in Material and Biological Sciences", Joint Institute for Nuclear Research, Dubna, Russia, September 9 – 12, 2012.
• A.H.Poghosyan, L.H. Arsenyan, A.A. Shahinyan "Molecular dynamics study of long chain alkyl sulfonate/water system", JCIS in review

Foreseen Activities

• Micelle self-assemble