A Workflow Management and Grid Computing Approach to Molecular Simulation-based Bio/Nano Experiments

Jeong, Karpjoo; Kim, Dongwook; Kim, Moon Hae; Hwang, Suntae; Jung, Seunho; Lim, Youngho; Lee, Sangsan

doi:10.1007/3-540-44864-0_116

Cited by 5 publications

(2 citation statements)

References 14 publications

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“…In addition to the development of these novel simulation techniques for the prediction of chiral discrimination, we have also constructed a computational Grid system called MGrid(http://service.mgrid.or.kr) [11]. This computing system is motivated by the large number of required force field calculations that are, in practice, impossible to handle with a single computer.…”

Section: Molecular Grid System (Mgrid)mentioning

confidence: 99%

A Grid Computing-Based Monte Carlo Docking Simulations Approach for Computational Chiral Discrimination

Choi

Kim

Hwang

et al. 2005

Lecture Notes in Computer Science

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Abstract.A validity of Grid computing with Monte Carlo (MC) docking simulations was examined in order to execute prediction and data handling for the computational chiral discrimination. Docking simulations were performed with various computational parameters for the chiral discrimination of a series of 17 enantiomers by β-cyclodextrin (β-CD) or by 6-amino-6-deoxy-β-cyclodextrin (am-β-CD). Rigid-body MC docking simulations gave more accurate predictions than flexible docking simulations. The accuracy was also affected by both the simulation temperature and the kind of force field. The prediction rate of chiral preference was improved by as much as 76.7% when rigid-body MC docking simulations were performed at low temperatures (100 K) with a sugar22 parameter set in the CHARMM force field. Our approach for Grid-based MC docking simulations suggested the conformational rigidity of both the host and guest molecule.

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Section: Molecular Grid System (Mgrid)mentioning

confidence: 99%

A Grid Computing-Based Monte Carlo Docking Simulations Approach for Computational Chiral Discrimination

Choi

Kim

Hwang

et al. 2005

Lecture Notes in Computer Science

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“…Efforts in the first category aim at building a user interface for legacy application programs such as CHARMM 1) and AMBER 2) . A user interface can be implemented as a portal on a Web server 3) or as a workflow management system executed on a client computer 4) . Such interfaces for MD simulations must enable users to monitor the progress of the remote computation, and we also have already reported a gridenabled application 5) that lets a user monitor the time evolution of a trajectory being produced by a MD application running on remote machines.…”

Section: Introductionmentioning

confidence: 99%

Implementation and Evaluation of Multiple GridRPC Services for Molecular Dynamics Simulations of Proteins

Amisaki

Fujiwara

2006

ipsjdc

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This paper reports a protein-simulation grid that uses grid remote procedure calls (GridR-PCs) to a special-purpose cluster machine for molecular dynamics simulations. The grid was implemented using Ninf-G, Torque, LAM, and the Globus Toolkit. To avoid the inefficiency of a single GridRPC session using all the nodes of the cluster, we designed the grid so that it works efficiently when multiple GridRPC sessions share the cluster. This was done by putting the dedicated nodes (PCs with special computation boards) under the management of the Torque system, thus enabling the manager to dynamically configure a cluster with the requested number of dedicated nodes. In addition, a new job type was added to the Globus toolkit and new backend procedure was added to Ninf-G. The Ninf-G stub was separated from processes that actually perform the force evaluation on the dedicated nodes. Simulations for two proteins gave promising results. Simulations performed using a four-node cluster and a 100-Mbps LAN for GridRPC sessions were 4.6-17.0 times faster than the same simulation performed on the local client PC, while their communication overhead was less than 20% of total execution time. Even when the the four-node cluster machine was shared between two distinct simulations of proteins, the two GridRPC communications did not interfere with each other. This showed the efficacy of multiple GridRPC sessions.

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Services for numerical simulations and optimisations in grids

Limmer

Schneider

Boehme

et al. 2013

International Journal of Parallel, Emergent and Distributed Sys

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Numerical simulations are typically very computer intensive. A way to satisfy the arising demands for compute power is the employment of grid technology. But today, there exist only a few tools supporting the user in using grids for numerical simulations. In addition, some basic problems of grid technology are not solved with satisfaction. The goal of the project OptiNum-Grid was to address these issues. We present a number of tools that were developed in the project. These are tools for parameter sweeps and optimisations in grids, for data security and automatic software installation, as well as for virtual environments in grids. The tools were evaluated in the context of three different use cases, namely finite element method simulations, analog circuit simulations and e-beam simulations

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A Workflow Management and Grid Computing Approach to Molecular Simulation-based Bio/Nano Experiments

Cited by 5 publications

References 14 publications

A Grid Computing-Based Monte Carlo Docking Simulations Approach for Computational Chiral Discrimination

A Grid Computing-Based Monte Carlo Docking Simulations Approach for Computational Chiral Discrimination

Implementation and Evaluation of Multiple GridRPC Services for Molecular Dynamics Simulations of Proteins

Services for numerical simulations and optimisations in grids

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