AMBER Archive (2008)

Subject: RE: AMBER: pmemd

From: Ross Walker (
Date: Thu Nov 20 2008 - 10:36:51 CST

Hi Jeremy,


It's very hard to work out what is going on here. Do you get any other error
messages? Any other output files at all?


I would start by asking for an interactive session. This is normally done
with something like:


qsub -i -nodes=.....


Then simply try mpirun -np ... on pmemd.


A few other things to check. Was pmemd compiled for parallel and using the
same lam mpi that you are running with here?


All the best




From: [] On Behalf Of
Jeremy Harris
Sent: Thursday, November 20, 2008 8:27 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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