Talk:Amber - Revision history

Tanthony@uab.edu: added data available at basic page

2012-07-16T17:14:58Z

added data available at basic page

← Older revision		Revision as of 17:14, 16 July 2012
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	</pre>		</pre>


			Some basic testing completed with data available at:http://ambermd.org/tutorials/basic/tutorial1/section3.htm

Tanthony@uab.edu: added sander commands

2012-07-16T16:39:05Z

added sander commands

@@ Line 58: / Line 58: @@
 <pre>
 Your job 82341234 ("ambertest_1") has been submitted
 </pre>

Tanthony@uab.edu: Sample amber submit script with qsub

2012-07-16T13:00:47Z

Sample amber submit script with qsub

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 Sample Job script for Amber
 <pre>
@@ Line 32: / Line 47: @@
 </pre>

Tanthony@uab.edu: Sample amber submit script

2012-07-16T12:57:15Z

Sample amber submit script

New page

Sample Job script for Amber

<pre>
#!/bin/bash
#$ -S /bin/bash
#
# Example Amber job submission script can be found here:
#
# Execute from the current working directory
#$ -cwd
#
# Job runtime (1 hour, at 55 minutes Amber will be notified to shut down)
#$ -l h_rt=1:00:00,s_rt=0:55:00
#$ -j y
#
# Job Name and email
#$ -N ambertest_1
#$ -M YOUR_EMAIL_ADDRESS
# Email options to determine when to send emails
#$ -m be
#
#$ -pe openmpi 4
#
# Load the appropriate module(s)
. /etc/profile.d/modules.sh
module load amber/amber-10-intel
#
#$ -V
#$ -l vf=1G
#
mpirun -np $NSLOTS $AMBERHOME/exe/sander.MPI -O -i file.in -o file.out -c file.restrt -p file.prmtop -r file.restrt -x file.cmd -ref file.restrt

</pre>