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American Chemical Society, Journal of Chemical Theory and Computation, 10(8), p. 3463-3472, 2012

DOI: 10.1021/ct300102d

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A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

Journal article published in 2012 by Marc van Dijk, Tsjerk A. Wassenaar, Alexandre M. J. J. Bonvin ORCID
This paper is available in a repository.
This paper is available in a repository.

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Abstract

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However, performing a successful simulation requires sufficient computational resources, familiarity with the simulation software, and experience in the setup of a system and the analysis of the resulting trajectories. These considerations become especially critical in large-scale parametric MD simulations. Offering such tools to a wide user community requires a robust and versatile, but user-friendly, facility for molecular dynamics simulations with access to vast computational resources. Here, we present the GROMACS grid-enabled Web portal for the setup and execution of molecular dynamics simulation on the WeNMR grid infrastructure, a distributed network of computational resources within the European Grid Initiative. T