Hi,
On Fri, Jan 24, 2014 at 2:00 AM, Saeed Nasiri <s.t.nasiri.gmail.com> wrote:
> =====================================================
> /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
> md1.dat
>
As Jason mentioned in his earlier response (
http://archive.ambermd.org/201401/0273.html) 'sander' is the serial version
of sander; if you want to run in parallel you need to run 'sander.MPI' (or
'pmemd.MPI'). Just replace 'sander' with 'sander.MPI'. If 'sander.MPI' is
not present, you need to re-configure in parallel (e.g. ./configure -mpi
gnu) and re-compile.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jan 24 2014 - 07:30:03 PST
