Dear AMBER
I have CSH script to run simulated annealing and it works fine. At the end
of simulated annealing (MD1). I wish to perform minimisation after
simulated annealing (MD1) and use this minimised "rst" output file as an
input for the MD2 simulation. Is there is a way to combine these two "csh
" script in to one.?
Simulated annealing script: MD1
=================================================================
#!/bin/csh
set AMBERHOME="/usr/local/amber"
set MDSTARTJOB=2
set MDENDJOB=50
set MDCURRENTJOB=$MDSTARTJOB
set MDINPUT=0
echo -n "Starting Script at: "
date
echo ""
while ( $MDCURRENTJOB <= $MDENDJOB )
echo -n "Job $MDCURRENTJOB started at: "
date
. MDINPUT = $MDCURRENTJOB - 1
mpirun -np 16 $AMBERHOME/bin/sander -O -i anneal.in \
-o mystrucuture_md$MDCURRENTJOB.out \
-p mystrucuture.prmtop \
-c mystrucuture_md$MDINPUT.rst \
-r mystrucuture_md$MDCURRENTJOB.rst \
-x mystrucuture_md$MDCURRENTJOB.mdcrd \
-inf mdinfo
gzip -9 -v mystrucuture_md$MDCURRENTJOB.mdcrd
echo -n "Job $MDCURRENTJOB finished at: "
date
. MDCURRENTJOB = $MDCURRENTJOB + 1
end
echo "ALL DONE"
===========================================================
I want to include in bellow script in to above script to also to perform
minimisation right after simulated annealing.
How to add following to ABOVE csh script
sander -O
-i min2.in
-o mystrucuture_min2_md$MDCURRENTJOB.out
-p mystrucuture.prmtop
-c mystrucuture_md$MDCURRENTJOB.rst (rst file from above MD1)
-r mystrucuture_min2_md$MDCURRENTJOB.rst (I want to use this file as an
input for MD2 run)
-x mystrucuture_min2_md$MDCURRENTJOB.mdcrd
Could anyone suggest me a way to include minimization to simulated
annealing script?
thanks in advance...
Best wishes
Vince
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Received on Wed Dec 16 2015 - 09:30:03 PST
