MDSCS

From HP-SEE Wiki

Revision as of 19:02, 23 March 2012

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 (MD) 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 MD 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, Germany
• International Center for Theoretical Physics, Italy

Beneficiaries

• Scientific Groups of the National Academy of Sciences of Armenia

Number of users

20

Development Plan

• Concept: Have been previously done
• Start of alpha stage: Have been previously done
• Start of beta stage: Successfully done
• Start of testing stage: Successfully done
• Start of deployment stage: Successfully done
• Start of production stage: in progress

Resource Requirements

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

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: .

Usage Example

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

Infrastructure Usage

• Home system: MDSCS
  • Applied for access on: 07.2011
  • Access granted on: 07.2011
  • Achieved scalability: 1024 cores
• Accessed production systems:

1. S/P by NAMD
   • Applied for access on: 07.2011
   • Access granted on: 07.2011
   • Achieved scalability: 1024 cores
2. S by GROMACS
   • Applied for access on: 08.2011
   • Access granted on: 08.2011
   • Achieved scalability: 512 cores

• Porting activities: .
• Scalability studies: .

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

Achieved Results

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

Publications

• 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.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 (accepted).
• 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