[AMBER] mpi-pmemd

From: Saeed Nasiri <s.t.nasiri.gmail.com>
Date: Fri, 24 Jan 2014 12:30:07 +0330

Dear Daniel Roe

Thanks for your helpful note. all of the action when compiling and running
amber are at the end of email.
Also in the first simulation there wasn't any problem in the md1.out file
but in the second simulation I saw some problems (
In addition I search about the pmemd.mpi command in the net and amber
document and I can't find any example for that. in the amber doc the
command was introduced. I don't know how to run?

Best regard

./configure intel
make install
make test
/home/s.nasiri/openmpi/bin/mpirun -np 64 -machinefile $PBS_NODEFILE sander
-O -i mdin.in -o md1.out -p ionicbox.prmtop -c min.x -r md1.x -x md1.nc -e
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Received on Fri Jan 24 2014 - 01:30:03 PST
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