Re: AMBER: pmemd

From: Robert Duke <>
Date: Thu, 20 Nov 2008 11:40:36 -0500

Well, at a minimum we would need the mdin input and info about the system (reflected in the prmtop/inpcrd) to even begin guessing. PMEMD does a lot of what sander does, but not everything (the differences are detailed in the manual). Also, presuming the executable for pmemd is good and the lam installation is good, you should have at least gotten some output in run11.out, or in your stderr file, wherever that is going. How many cpu's are you attempting to use? How many did you use for sander.MPI?
Regards - Bob Duke
  ----- Original Message -----
  From: Jeremy Harris
  Sent: Thursday, November 20, 2008 11:27 AM
  Subject: AMBER: pmemd


  I am simulating a protein in explicit water, and I've been using sander with lamwrapper, but want to use pmemd, as I understand it is faster. However, I've been having trouble running the jobs. I'm not sure where to start with this, so any help would be appreciated.

  My submission script is:

  #PBS -N run11
  #PBS -q s2
  #PBS -l walltime=00:15:00
  #Write usefull things to the output file
  echo "Starting job $PBS_JOBID"
  echo "PBS assigned these nodes:"
  echo First task running on:
  uname -a
  echo at
  export PATH=/usr/local/amber9:$PATH
  /usr/local/bin/lamwrapper -- /usr/local/amber9/exe/pmemd -O -i -o run11.out -p 1CDL_wat.prmtop -c run10.rst -r run11.rst -x run11.mdcrd

  The output file is:

  PBS assigned these nodes:

  First task running on:
  Linux comp00 #1 SMP Tue Jan 10 16:02:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux
  Thu Nov 20 15:53:18 GMT 2008

  LAM 7.1.1/MPI 2 C++/ROMIO - Indiana University

  No dedicated nodes so no cleanup done.

  Thanks in advance,
  Jeremy Harris

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Received on Fri Dec 05 2008 - 16:10:25 PST
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