Amber: Difference between revisions
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====Use Amber on the Cheaha==== | |||
A '''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 16:02, 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
A untested job submit script for Amber is avaialble at: https://docs.uabgrid.uab.edu/wiki/Talk:Amber