Application of grid computing to parameter sweeps and optimizations in molecular modeling

Authors:
Wibke Sudholt;Kim K. Baldridge;David Abramson;Colin Enticott;Slavisa Garic;Chris Kondric;Duy Nguyen
Affiliations:
Institute of Organic Chemistry, University of Zürich, 190 Winterthurerstrasse, Zürich 8057, Switzerland;Institute of Organic Chemistry, University of Zürich, 190 Winterthurerstrasse, Zürich 8057, Switzerland and San Diego Supercomputer Center (SDSC), University of California, San Diego (UC ...;Center for Enterprise Distributed Systems (DSTC), Monash University, Clayton, Victoria, 3800 Australia;Center for Enterprise Distributed Systems (DSTC), Monash University, Clayton, Victoria, 3800 Australia;Center for Enterprise Distributed Systems (DSTC), Monash University, Clayton, Victoria, 3800 Australia;San Diego Supercomputer Center (SDSC), University of California, San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093-0505, USA and Center for Enterprise Distributed Systems (DSTC), Monash Univ ...;San Diego Supercomputer Center (SDSC), University of California, San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093-0505, USA and Center for Enterprise Distributed Systems (DSTC), Monash Univ ...
Venue:
Future Generation Computer Systems
Year:
2005

Citing 0
Cited 10

Special section: Medical imaging on grids

Future Generation Computer Systems
Large-scale functional MRI study on a production grid

Future Generation Computer Systems
Chemomentum - UNICORE 6 based infrastructure for complex applications in science and technology

Euro-Par'07 Proceedings of the 2007 conference on Parallel processing
Using a private desktop grid system for accelerating drug discovery

Future Generation Computer Systems
Exploiting grid technologies for the simulation of clinical trials: the paradigm of in silico radiation oncology

Simulation
Scientific workflow infrastructure for computational chemistry on the grid

ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part III
A framework for execution of computational chemistry codes in grid environments

ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part III
Applications development for the computational grid

APWeb'06 Proceedings of the 8th Asia-Pacific Web conference on Frontiers of WWW Research and Development
A framework for the design and reuse of grid workflows

SAG'04 Proceedings of the First international conference on Scientific Applications of Grid Computing
Scheduling parameter sweep workflow in the Grid based on resource competition

Future Generation Computer Systems

Quantified Score

Hi-index	0.00

Visualization

Abstract

In science and engineering in general and in computational chemistry in particular, parameter sweeps and optimizations are of high importance. Such parametric modeling jobs are embarrassingly parallel and thus well suited for grid computing. The Nimrod toolkit significantly simplifies the utilization of computational grids for this kind of research by hiding the complex grid middleware, automating job distribution, and providing easy-to-use user interfaces. Here, we present examples for the usage of Nimrod in molecular modeling. In detail, we discuss the parameterization of a group difference pseudopotential (GDP). Other applications are protein-ligand docking and a high-throughput workflow infrastructure for computational chemistry.