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VMD

VMD is a molecular visualisation program for displaying, animating, and analysing large biomolecular systems using 3-D graphics and built-in scripting. The two software packages available on our Service that can interface with VMD are AMBER and NAMD.

Detailed online tutorials for using VMD with AMBER and NAMD are available from the AMBER and NAMD web sites.

AMBER: http://ambermd.org/

NAMD: http://www.ks.uiuc.edu/Research/namd/

Please note that AMBER and NAMD jobs cannot be run interactively via VMD. All jobs should be submitted via the LSF batch queues.

VMD is available on Magellan and can be accessed by using the runscript $CHEM/runvmd. For more details, please read the man page by typing: man runvmd.

 

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