AMBER Archive (2008)

Subject: AMBER: pmemd

From: Jeremy Harris (jphillipharris_at_gmail.com)
Date: Thu Nov 20 2008 - 10:27:14 CST

Hello,

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
cd $PBS_O_WORKDIR
#
#Write usefull things to the output file
#
echo "Starting job $PBS_JOBID"
echo
echo "PBS assigned these nodes:"
cat $PBS_NODEFILE
echo
#
echo First task running on:
uname -a
echo at
date
#
export PATH=/usr/local/amber9:$PATH
/usr/local/bin/lamwrapper -- /usr/local/amber9/exe/pmemd -O -i run.in -o
run11.out -p 1CDL_wat.prmtop -c run10.rst -r run11.rst -x run11.mdcrd

The output file is:

PBS assigned these nodes:
comp00
comp00

First task running on:
Linux comp00 2.6.11.4-21.10-1SCORE-smp #1 SMP Tue Jan 10 16:02:23 GMT 2006
x86_64 x86_64 x86_64 GNU/Linux
at
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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