Title: On the extension of the grid-empowered molecular science simulator: MD and visualisation tools

Authors: Alessandro Costantini, Eduardo Gutierrez, Javier Lopez Cacheiro, Aurelio Rodriguez, Osvaldo Gervasi, Antonio Lagana

Addresses: Department of Chemistry, Department of Mathematics and Computer Science, University of Perugia, via Elce di Sotto 8, 06100 Perugia, Italy. ' CESGA, Santiago de Compostela Avenida de Vigo, s/n Campus Sur, 15705, Spain. ' CESGA, Santiago de Compostela Avenida de Vigo, s/n Campus Sur, 15705, Spain. ' CESGA, Santiago de Compostela Avenida de Vigo, s/n Campus Sur, 15705, Spain. ' Department of Mathematics and Computer Science, University of Perugia, via Vanvitelli 1, 06100 Perugia, Italy. ' Department of Chemistry, University of Perugia, via Elce di Sotto 8, 06100 Perugia, Italy

Abstract: The central block of the Grid Empowered Molecular Simulator GEMS was extended to Molecular Dynamics calculations by implementing the GROMACS code. The Grid porting was carried out using the P-GRADE Portal tool. The performances achieved using this approach were measured and compared with those of other approaches better exploiting the mixed nature of the computing resources available on the Grid. The work was completed by implementing some Grid based graphical rendering utilities and extending the study to another Molecular Dynamics package.

Keywords: workflows; grid computing; grid portals; GROMACS package; molecular dynamics; simulation; molecular science.

DOI: 10.1504/IJWGS.2010.033789

International Journal of Web and Grid Services, 2010 Vol.6 No.2, pp.141 - 159

Published online: 30 Jun 2010 *

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