From UABgrid Documentation
(added category MD, chemistry)
(added link to untested Amber job script)
|Line 21:||Line 21:|
Revision as of 10:02, 16 July 2012
This page is a Generic stub.
You can help by expanding this page..
"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):
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