Amber - Revision history

Tanthony@uab.edu: added the submit script from the discussion page

2012-07-16T17:31:40Z

added the submit script from the discussion page

@@ Line 22: / Line 22: @@
 ====Use Amber on the Cheaha====
-An '''untested''' job submit script for Amber is avaialble at: https://docs.uabgrid.uab.edu/wiki/Talk:Amber
+Sample Job script for Amber
 [[Category:Software]][[Category:Molecular Dynamics]][[Category:Chemistry]]

2012-07-16T16:11:35Z

Use Amber on the Cheaha

← Older revision		Revision as of 16:11, 16 July 2012
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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		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]]

2012-07-16T16:02:12Z

added link to untested Amber job script

← Older revision		Revision as of 16:02, 16 July 2012
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	</pre>		</pre>

			====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]]

2012-04-04T14:56:50Z

added category MD, chemistry

← Older revision		Revision as of 14:56, 4 April 2012
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	[[Category:Software]]		[[Category:Software]][[Category:Molecular Dynamics]][[Category:Chemistry]]

2012-04-04T13:42:26Z

added category software

2012-04-02T19:37:45Z

adde link

← Older revision		Revision as of 19:37, 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.		[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:'''		'''Project website:''' http://ambermd.org/

	====Load SGE module====		====Load SGE module====

2012-04-02T19:36:57Z

← Older revision		Revision as of 19:36, 2 April 2012
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	'''Project website:'''		'''Project website:'''

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

2012-04-02T18:09:53Z

← Older revision		Revision as of 18:09, 2 April 2012
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	~~/opt/uabeng/amber10/intel~~		"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" 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:'''

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

2012-03-15T15:52:59Z

added from Mike's software table

← Older revision		Revision as of 15:52, 15 March 2012
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	{{Generic_stub}}		{{Generic_stub}}


			/opt/uabeng/amber10/intel
			\|"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.

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

			For Intel:
			<pre>
			module load amber/amber-10-intel
			</pre>

			Use the '''openmpi''' parallel environment in your job script (example for a 4 slot job)
			<pre>
			#$ -pe openmpi 4
			</pre>

2012-03-15T15:34:26Z

created page with generic stub

New page