Gromacs - Revision history

Mhanby@uab.edu at 19:51, 31 October 2016

2016-10-31T19:51:37Z

← Older revision		Revision as of 19:51, 31 October 2016
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	<pre>		<pre>
	$ mkdir -p ~~/scratch/user/USERNAME~~/jobs/gromacs		$ mkdir -p $USER_SCRATCH/jobs/gromacs
	$ cd ~~/scratch/user/USERNAME~~/jobs/gromacs		$ cd $USER_SCRATCH/jobs/gromacs
	</pre>		</pre>

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	Copy the directory "d.dppc" from the local host to a remote host's directory "gromacs"		Copy the directory "d.dppc" from the local host to a remote host's directory "gromacs"
	<pre>		<pre>
	$ scp -r d.dppc USERNAME@cheaha.uabgrid.uab.edu:/scratch~~/user~~/USERNAME/jobs/gromacs		$ scp -r d.dppc USERNAME@cheaha.uabgrid.uab.edu:/data/scratch/USERNAME/jobs/gromacs
	</pre>		</pre>

2013-06-19T19:27:15Z

Submitting Gromacs jobs to Cheaha

← Older revision		Revision as of 19:27, 19 June 2013
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	<pre>		<pre>
	$ mkdir -p /~~lustre~~/~~scratch~~/USERNAME/jobs/gromacs		$ mkdir -p /scratch/user/USERNAME/jobs/gromacs
	$ cd /~~lustre~~/~~scratch~~/USERNAME/jobs/gromacs		$ cd /scratch/user/USERNAME/jobs/gromacs
	</pre>		</pre>

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	Copy the directory "d.dppc" from the local host to a remote host's directory "gromacs"		Copy the directory "d.dppc" from the local host to a remote host's directory "gromacs"
	<pre>		<pre>
	$ scp -r d.dppc USERNAME@cheaha.uabgrid.uab.edu:/~~lustre~~/~~scratch~~/USERNAME/jobs/gromacs		$ scp -r d.dppc USERNAME@cheaha.uabgrid.uab.edu:/scratch/user/USERNAME/jobs/gromacs
	</pre>		</pre>

2012-04-04T14:57:57Z

added category MD

← Older revision		Revision as of 14:57, 4 April 2012
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	[[Category: ~~Gromacs~~]][[Category:~~Software~~]]		[[Category:Software]][[Category:Molecular Dynamics]]

2012-04-04T14:00:21Z

added category software

← Older revision		Revision as of 14:00, 4 April 2012
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	[[Category: Gromacs]]		[[Category: Gromacs]][[Category:Software]]

2011-06-14T17:00:15Z

← Older revision		Revision as of 17:00, 14 June 2011
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	[http://www.gromacs.org/ Gromacs] is a molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. originally developed in the '''[[wikipedia:University of Groningen\|University of Groningen]]''', now maintained and extended at different places, including the '''[[wikipedia:University of Uppsala\|University of Uppsala]]''', '''[[wikipedia:University of Stockholm\|University of Stockholm]]''' and the [[Max Planck Institute for Polymer Research]].		[http://www.gromacs.org/ Gromacs] is a molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. originally developed in the '''[[wikipedia:University of Groningen\|University of Groningen]]''', now maintained and extended at different places, including the '''[[wikipedia:University of Uppsala\|University of Uppsala]]''', '''[[wikipedia:University of Stockholm\|University of Stockholm]]''' and the '''[[wikipedia:Max Planck Institute for Polymer Research\|Max Planck Institute for Polymer Research]]'''.
	GROMACS is '''[[wikipedia:open source\|open source]]''' software released under the '''[[wikipedia:GNU General Public License\|GPL]]'''.		GROMACS is '''[[wikipedia:open source\|open source]]''' software released under the '''[[wikipedia:GNU General Public License\|GPL]]'''.

2011-06-14T16:59:09Z

Gromacs on Your Desktop

← Older revision		Revision as of 16:59, 14 June 2011
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	=== Gromacs on Your Desktop ===		=== Gromacs on Your Desktop ===
	Gromacs can be downloaded and installed on your desktop from http://www.gromacs.org/.		Gromacs can be downloaded and installed on your desktop from http://www.gromacs.org/.

	Linux: Download and installation instructions for Gromacs are available at: http://www.gromacs.org/Downloads/Installation_Instructions		Linux: Download and installation instructions for Gromacs are available at: http://www.gromacs.org/Downloads/Installation_Instructions

	Windows: Download and installation instructions for Gromacs on Windows are avialable at: http://www.gromacs.org/Downloads/Installation_Instructions/Windows		Windows: Download and installation instructions for Gromacs on Windows are avialable at: http://www.gromacs.org/Downloads/Installation_Instructions/Windows

2011-06-14T16:57:47Z

Submitting Gromacs jobs to Cheaha

← Older revision		Revision as of 16:57, 14 June 2011
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	#$ -M tanthony@uab.edu		#$ -M tanthony@uab.edu
	#		#
	#$ -pe openmpi* 32		#$ -pe openmpi* 8
	# Load the appropriate module(s)		# Load the appropriate module(s)
	. /etc/profile.d/modules.sh		. /etc/profile.d/modules.sh
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	The job output can be found in the output directory specified earlier.		The job output can be found in the output directory specified earlier.


	== Gromacs Support ==		== Gromacs Support ==

2011-06-14T16:57:11Z

minor edits and cleaning up

← Older revision		Revision as of 16:57, 14 June 2011
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	* -l vf to the maximum memory needed for each task		* -l vf to the maximum memory needed for each task
	* cd to the current working directory where the job data is stored		* cd to the current working directory where the job data is stored
	* ~~export MYFILE=configFileName (export MYFILE=apoa1 willuse config~~ file ~~apoa1~~		* input file is topol.tpr, output file is gromacs_numberOfProcessors.out

	<pre>		<pre>

2011-06-14T16:52:26Z

← Older revision		Revision as of 16:52, 14 June 2011
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	Benchmark data for running Gromacs on [[Cheaha]] will be developed leveraging the benchmark foundation of the [http://biowulf.nih.gov/apps/gromacs NIH's Biowulf cluster Gromacs] testing suite combined with local work flow characteristics.		Benchmark data for running Gromacs on [[Cheaha]] will be developed leveraging the benchmark foundation of the [http://biowulf.nih.gov/apps/gromacs NIH's Biowulf cluster Gromacs] testing suite combined with local work flow characteristics.
	A comparative benchmark between the UAB Cheaha cluster, NIH Biowulf cluster and the ASC's Dense Memory Cluster has been performed and the results are available [[Gromacs ~~Benchmarks~~\|here]].		A comparative benchmark between the UAB Cheaha cluster, NIH Biowulf cluster and the ASC's Dense Memory Cluster has been performed and the results are available [[Gromacs Benchmark\|here]].

2011-06-14T16:52:00Z

← Older revision		Revision as of 16:52, 14 June 2011
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	* Gormacs Tutorials can be found at: http://www.gromacs.org/Documentation/Tutorials		* Gormacs Tutorials can be found at: http://www.gromacs.org/Documentation/Tutorials
	* Gromacs Tutorials: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html		* Gromacs Tutorials: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
	* Gromacs Introduction: www-personal.umich.edu/~amadi/fwspidr_tutor.pdf		* Gromacs Introduction: http://www-personal.umich.edu/~amadi/fwspidr_tutor.pdf


	== Benchmarks ==		== Benchmarks ==

	~~=== 2011 Hardware ===~~

	Benchmark data for running Gromacs on [[Cheaha]] will be developed leveraging the benchmark foundation of the [http://biowulf.nih.gov/apps/gromacs NIH's Biowulf cluster Gromacs] testing suite combined with local work flow characteristics.		Benchmark data for running Gromacs on [[Cheaha]] will be developed leveraging the benchmark foundation of the [http://biowulf.nih.gov/apps/gromacs NIH's Biowulf cluster Gromacs] testing suite combined with local work flow characteristics.