AppTemp

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	== General Information ==		== General Information ==
-	* Application's name: ''Molecular Dynamics Study of Complex Systems (MDSCS)''	+	* Application's name:
-	* Application's acronym: ''MDSCS''	+	* Application's acronym:
-	* Virtual Research Community: ''VRC "Life Sciences"''	+	* Virtual Research Community: ''VRC
-	* Scientific contact: ''Dr. Armen Poghosyan, sicnas@sci.am''	+	* Scientific contact:
-	* Technical contact: ''Dr. Hrachya Astsatryan, hrach@sci.am''	+	* Technical contact:
-	* Developers: ''National Academy of Sciences of the Republic of Armenia ''	+	* Developers:
	* Web site: ...		* Web site: ...
	== Short Description ==		== 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 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 molecular dynamics (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 ==		== Problems Solved ==
-	The 50ns MD 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 MD 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 ==		== 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 ==		== Collaborations ==
-	* Institut für Chemie of Universität Potsdam, Germany	+	*
-	* International Center for Theoretical Physics, Italy	+
	== Beneficiaries ==		== Beneficiaries ==
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	== Development Plan ==		== Development Plan ==
-	* Concept: ''Have been previously done''	+	* Concept:
-	* Start of alpha stage: ''Have been previously done''	+	* Start of alpha stage:
-	* Start of beta stage: ''Successfully done''	+	* Start of beta stage:
-	* Start of testing stage: ''Successfully done''	+	* Start of testing stage:
-	* Start of deployment stage: ''in progress''	+	* Start of deployment stage:
-	* Start of production stage: ''in progress''	+	* Start of production stage:
	== Resource Requirements ==		== Resource Requirements ==
-	* Number of cores required for a single run: ''up to 1024''	+	* Number of cores required for a single run:
-	* Minimum RAM/core required: ''2/4GB''	+	* Minimum RAM/core required:
-	* Storage space during a single run: ''0.5TB''	+	* Storage space during a single run:
-	* Long-term data storage: ''5TB''	+	* Total core hours required:
-	* Total core hours required: ''...''	+
	== Technical Features and HP-SEE Implementation ==		== Technical Features and HP-SEE Implementation ==
-	* Primary programming language: ''C/C++ ''	+	* Primary programming language:
-	* Parallel programming paradigm: ''MPI/OpenMP ''	+	* Parallel programming paradigm:
-	* Main parallel code: ''NAMD,GROMACS''	+	* Main parallel code:
-	* Pre/post processing code: ''...''	+	* Pre/post processing code:
-	* Application tools and libraries: ''...''	+	* Application tools and libraries:
	== Usage Example ==		== Usage Example ==
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	== Infrastructure Usage ==		== Infrastructure Usage ==
-	* Home system: ''MDSCS''
-	** Applied for access on: ''07.2011''
-	** Access granted on: ''07.2011''
-	** Achieved scalability: ''1024 cores''
-	* Accessed production systems:
-	# ''S/P by NAMD''
-	#* Applied for access on: ''07.2011''
-	#* Access granted on: ''07.2011''
-	#* Achieved scalability: ''1024 cores''
-	# ''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 ==		== 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''.
-	* Other issues: ''...''
	== Achieved Results ==		== Achieved Results ==
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	== Publications ==		== Publications ==
-	* A.H. Poghosyan, L. H. Arsenyan, H. Astsatryan, M. Gyurjyan, H. Keropyan, A.A.Shahinyan "NAMD Package Benchmarking on the Base of Armenian Grid Infrastructure" ''Communication & Network,'' '''in press''', 2011.	+
	* ...		* ...

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Revision as of 19:48, 26 December 2011

Contents 1 General Information 2 Short Description 3 Problems Solved 4 Scientific and Social Impact 5 Collaborations 6 Beneficiaries 7 Number of users 8 Development Plan 9 Resource Requirements 10 Technical Features and HP-SEE Implementation 11 Usage Example 12 Infrastructure Usage 13 Running on Several HP-SEE Centres 14 Achieved Results 15 Publications 16 Foreseen Activities

General Information

• Application's name:
• Application's acronym:
• Virtual Research Community: VRC
• Scientific contact:
• Technical contact:
• Developers:
• Web site: ...

Short Description

Problems Solved

Scientific and Social Impact

Collaborations

Beneficiaries

• ...
• ...

Number of users

...

Development Plan

• Concept:
• Start of alpha stage:
• Start of beta stage:
• Start of testing stage:
• Start of deployment stage:
• Start of production stage:

Resource Requirements

• Number of cores required for a single run:
• Minimum RAM/core required:
• Storage space during a single run:
• Total core hours required:

Technical Features and HP-SEE Implementation

• Primary programming language:
• Parallel programming paradigm:
• Main parallel code:
• Pre/post processing code:
• Application tools and libraries:

Usage Example

...

Infrastructure Usage

Running on Several HP-SEE Centres

Achieved Results

...

Publications

• ...

Foreseen Activities

• ...
• ...