Hi amber users,
I think there is a mistake in the script
run_a-dna_20-1820ps.x
on the tutorial web site:
http://amber.scripps.edu/tutorial/polyA-polyT_New/adna.html
The text says that the total 1.8ns run will be executed by running 9 x 200
ps simulations with each successive
simulation continuing on from the previous one.
The script submits all the 9 simulations at the same time and not
successively!
Ioana
Here is what I would propose:
use crontab to run the script.csh every 30 minutes:
30 * * * * $PATH/script.csh
Content of:
script.csh
****************************************
#!/bin/csh
set AMBERHOME="/usr/local/AMBER8"
set MDSTARTJOB=2
set MDENDJOB=10
set MDCURRENTJOB=$MDSTARTJOB
set MDINPUT=0
echo -n "Starting Script at: "
date
echo ""
set user = `whoami`
while ( $MDCURRENTJOB <= $MDENDJOB )
set chk = `ps -u $user |grep sander | wc -l`
if ($chk == 0) then
echo -n "Job $MDCURRENTJOB started at: "
date
. MDINPUT = $MDCURRENTJOB - 1
$AMBERHOME/exe/sander -O -i a-dna_md_1800ps.in \
-o a-dna_md$MDCURRENTJOB.out \
-p a-dna_wat.prmtop \
-c a-dna_md$MDINPUT.rst \
-r a-dna_md$MDCURRENTJOB.rst \
-x a-dna_md$MDCURRENTJOB.mdcrd
gzip -9 -v a-dna_md$MDCURRENTJOB.mdcrd
echo -n "Job $MDCURRENTJOB finished at: "
date
. MDCURRENTJOB = $MDCURRENTJOB + 1
endif
end
echo "ALL DONE"
******************
Ioana Cozmuta, PhD
Research Scientist
Eloret Corporation
Mail Stop 230-3
NASA AMES Research Center,
Moffet Field, CA 94035-1000
Phone: (650) 604-0993
http://www.ipt.arc.nasa.gov/computationalpeople.html
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Received on Fri Apr 09 2004 - 03:53:00 PDT
