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Amber

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(added link to untested Amber job script)
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====Use Amber on the Cheaha====
 
====Use Amber on the Cheaha====
A '''untested''' job submit script for Amber is avaialble at: https://docs.uabgrid.uab.edu/wiki/Talk:Amber
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An '''untested''' job submit script for Amber is avaialble at: https://docs.uabgrid.uab.edu/wiki/Talk:Amber
  
 
[[Category:Software]][[Category:Molecular Dynamics]][[Category:Chemistry]]
 
[[Category:Software]][[Category:Molecular Dynamics]][[Category:Chemistry]]

Revision as of 10:11, 16 July 2012

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"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

Amber is compiled using Intel compilers and uses OpenMPI for the parallel binaries.

Project website: http://ambermd.org/

Load SGE module

The following Modules files should be loaded for this package (the amber module will automatically load the openmpi module):

For Intel:

module load amber/amber-10-intel

Use the openmpi parallel environment in your job script (example for a 4 slot job)

#$ -pe openmpi 4

Use Amber on the Cheaha

An untested job submit script for Amber is avaialble at: https://docs.uabgrid.uab.edu/wiki/Talk:Amber