Re: [AMBER] bash scripting for MD tasks

From: James Starlight <>
Date: Fri, 26 Sep 2014 11:43:22 +0200

Dear all,

I wounder to ask some suggestions about possibility to improve my launch
script aimed on the running of several similations.

e.g my current protocol use simple looping over the dir with the
simulations to run sh file in each folder which is call for the pmemd etc
for each system


# set workdir with proteins

#run each simulation
for sim in $simulations/* ; do
  simulation=$(basename "$sim")
  echo "Simulation of ${simulation} is in a progress!"
  cd $sim
  chmod +x ./${simulation}.Sh
  echo "Simulation of ${simulation} has been finished"

how this script can be improved to i) avoid call sh from the another sh?
ii) to run several jobs in parallel corresponded to the number of available
GPU of my workstation ?

Thanks for help,

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Received on Fri Sep 26 2014 - 03:00:03 PDT
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