I've played around with a script in the ross walker tutorial to see
whether it would be possible to run my own simulation. Basically you'd
input a filename. The files necessary for a heating would be run and
used to generate rst files for the eq phase of the simulation which
would run in a loop five times . Since I don't have good exp making
scripts I'd like to present what I have so far here to see whether
there are any mistakes.. I tried to refrain from changing the original
script as much as possible. I'm not sure whether the filenames I'm
using would work.
#!/bin/csh
set AMBERHOME="/usr/local/AMBER8"
set MDSTARTJOB=2
set MDENDJOB=6
set MDCURRENTJOB=$MDSTARTJOB
set MDINPUT=1
echo -n "enter filename"
$filename=<STDIN>
chop($filename);
echo -n "Starting Script at: "
date
echo ""
echo -n "Warming started at: "
date
$AMBERHOME/exe/sander -O -i hot.in \
-o hot$filename.out \
-p $filename.prmtop \
-c $filename.rst \
-r $filename$MDINPUT.rst \
-x hot$filename.mdcrd
echo -n "Job hot$filename finished at: "
date
while ( $MDCURRENTJOB <= $MDENDJOB )
echo -n "Job $MDCURRENTJOB started at: "
date
. MDINPUT = $MDCURRENTJOB - 1
$AMBERHOME/exe/sander -O -i mdp53.in \
-o $filename$MDCURRENTJOB.out \
-p $filename.prmtop \
-c $filename$MDINPUT.rst \
-r $filename$MDCURRENTJOB.rst \
-x $filename$MDCURRENTJOB.mdcrd
gzip -9 -v $filename$MDCURRENTJOB.mdcrd
echo -n "Job $MDCURRENTJOB finished at: "
date
. MDCURRENTJOB = $MDCURRENTJOB + 1
end
echo "ALL DONE"
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Received on Sun Feb 19 2006 - 06:10:09 PST
