Dear Amber and scripting experts,
I have very humble knowledge about script languages so I seek some help. I
am running umbrella sampling calculation so I have to make sander read from
sequential external files (restraint files) using some script available on
([1]
http://projects.eml.org/mcm/people/wang/PMF/tutorial.html).Thepointis
this script needs tcsh shell ( the scripts starts with #!/bin/tcsh) and that
causes some conflict with the other commands required to run the job in
parallel (see below the script that we use to submit the jobs on our
cluster) so when I added the bit required for PMF calculation, the (
PBS_NODEFILE: nproc) commands do not like this bit to be in the same file
The added lines are highlighted in red (these lines need for PMF calculation
while the rest of the script is used to submit the jobs in parallel.
Any idea from more scripts experienced people to let me know how to avoid
this conflict??
#!/bin/tcsh
###These lines are for Moab
#MSUB -l nodes=2:ppn=8
#MSUB -l partition=ALL
#MSUB -l walltime=400:00:00
#MSUB -m be
#MSUB -V
#MSUB -o
/export/home/msoliman/scratch/Amber/glycosidase_work/pmf/AM1/amber.our
#MSUB -e
/export/home/msoliman/scratch/Amber/glycosidase_work/pmf/AM1/amber.err
#MSUB -d /export/home/msoliman/scratch/Amber/glycosidase_work/pmf/AM1/
#MSUB -mb
set number=(3.2 3.0 2.8 2.6 2.4 2.2 2.0 1.8 1.6 1.4 1.2 1.0)
foreach N ($number)
sed -e 's/minimum/'$N'/g' umbrella.in > input.in
##### Running commands
####nproc=`wc $PBS_NODEFILE | awk '{print $1}'`
exe=/export/home/nmonama/amber/bin/sander.MPI
nproc=`cat $PBS_NODEFILE | wc -l`
mpirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i input.in -o
dist_$N.out -p com_solvated.top -c com_solvated_equil.qmmm.rst -r
dist_$N.xyz -x dist_$N.trj
Thanks
Mahmoud
References
1.
http://projects.eml.org/mcm/people/wang/PMF/tutorial.html
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Received on Tue Mar 29 2011 - 14:30:03 PDT
