Dear AMBER Netters,
I have a question about the use of PMEMD. It is probably a trivial
question, but, as I did not find an answer neither on the Web pages
neither in the manuals, I am asking it to you.
I am doing the parallel calculations with sander.MPI using a lamd deamon
and the command nohup to launch the job, so I am doing:
. /Bis/shared/centos-3_x86_64/etc/custom.d/amber9_intel8.1_lam-7.1.2_intel-8.1.sh
lamboot
before starting the AMBER calculations. The typical command line for
sander.MPI is then:
mpirun -np 4 ${AMBERHOME}/exe/sander.MPI -O -i mdr1.in -o mdr1.out -inf mdr1.inf -x mdr1.crd -c eq7.rst -p prmtop -r mdr1.rst
But, if I replace in the command line sander.MPI by pmemd.MPI:
mpirun -np 4 ${AMBERHOME}/exe/pmemd.MPI -O -i mdr1.in -o mdr1.out -inf mdr1.inf -x mdr1.crd -c eq7.rst -p prmtop -r mdr1.rst
I get an error saying that lamboot was not started.
I am trying to do these calculation on an 64 bits 8-proc Linux machine,
running under centos-3. The lam used is the version 7.1.2_intel-8.1.
Also, I am only using features which should exist in PMEMD according to
the AMBER manual.
Do you have any idea what I could check or what to find information to fix
this problem?
Thank you in abvance for your help,
Therese Malliavin
Unite de Bioinformatique Structurale
Institut Pasteur, Paris
France
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Received on Wed Dec 17 2008 - 01:10:00 PST
