Re: [AMBER] script problem

From: Mahmoud Soliman <>
Date: Tue, 29 Mar 2011 23:44:46 +0200

   On 3/29/11 11:15 PM, Jason Swails wrote:

Googling "tcsh help" leads you to the site [1] .
That's a fairly comprehensive review of tcsh scripting.

If you're familiar with another shell (e.g. bash), then try rewriting that
script in bash instead. It'll help strengthen your scripting ability while
helping you to understand the steps that the script is actually taking.

   I will try

One thing I would suggest, however, is not to run a 400 hour job before you
have a firm grasp of what you're doing. Run short jobs with small time
limits (nstlim=1000, or something) just to make sure you have a grasp of
what's happening before you dump that much computing power on the problem.

   I do agree with you, thanks for your advice
   Best wishes

Good luck,

On Tue, Mar 29, 2011 at 2:16 PM, Mahmoud Soliman [2]<>wro

  Dear Amber and scripting experts,
  I have very humble knowledge about script languages so I seek some help.
  am running umbrella sampling calculation so I have to make sander read
  sequential external files (restraint files) using some script available
  this script needs tcsh shell ( the scripts starts with #!/bin/tcsh) and
  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
  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??
  ###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
  #MSUB -e
  #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' >
  ##### Running commands
  ####nproc=`wc $PBS_NODEFILE | awk '{print $1}'`
  nproc=`cat $PBS_NODEFILE | wc -l`
  mpirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i -o
  dist_$N.out -p -c com_solvated_equil.qmmm.rst -r
  dist_$ -x dist_$N.trj



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   Mahmoud E. Soliman

   Computational Chemistry & Modeling (PhD)

   Department of Chemistry

   University of Bath


   BA2 7AY

   United Kingdom




   Mahmoud E. Soliman

   Lecturer of pharmaceutical organic chemistry

   Pharmaceutical Organic Chemistry Dept.

   Faculty of pharmacy

   Zagazig University









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Received on Tue Mar 29 2011 - 15:00:02 PDT
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