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Amber

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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.
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[http://ambermd.org/ "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.
 
Amber is compiled using Intel compilers and uses OpenMPI for the parallel binaries.
  
'''Project website:'''
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'''Project website:''' http://ambermd.org/
  
 
====Load SGE module====
 
====Load SGE module====

Revision as of 13:37, 2 April 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