NGS/CCPB Workshop - Running simulations on the NGS

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The first joint NGS/CCPB Training Workshop was held at the National e-Science Centre, Edinburgh on 25th November 2008.

This workshop gave an introduction to grid computing and the National Grid Service (NGS), followed by a step-by-step guide to running simulations using the MD codes available on the NGS (AMBER, NAMD, GROMACS). This included tutorials on job submission via the Globus Toolkit and via the NGS Portal.

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Presentations and tutorials provided by the NGS for this event can be found here. You will note that these documents discuss using temporary grid certificates and accounts, these have now expired. To be able to follow these tutorials you will need to sign up for your own certificate and account, this is easily done by going to the following website: http://www.grid-support.ac.uk/content/view/240/159/ and following the instructions for potential users

Two further tutorials are available from the workshop, which give instructions on how to run AMBER, NAMD and GROMOCS simulations on the NGS. The data required to run these simulations (starting structures, parameter and input files) were installed on the training computers for the workshop, but all this information can be downloaded here.

Tutorial 1 guides you through running simulations on the NGS using the Globus Toolkit, all three simulation codes are included.

Tutorial 2 guides you through running a number of simulations simultaneously using the NGS Portal (AMBER only).