N-J.M. Macaluso wrote:
Hello,
I have a question regarding replica exchange MD in Gromacs. I think I
am preparing all of the files in the correct fashion, but I continually
get the same error message.
Here is what I'm doing. I prepared three different mdp files, each
specifying a specific temperature (PME0.mdp, PME1.mdp, and PME2.mdp).
Then I grompp the energy minimized peptide I want to simulate:
grompp -f PME0.mdp -po PME0out.mdp -c peptide.gro -p peptide.top -o
peptide0.tpr -np 4
you can only run each replica on one processor in 3.3
After this, I submit the simulation via an MPI queueing system. The
mdrun command looks like this:
mdrun_mpi -replex 1000 -s peptide.tpr -np 4 -o peptide.trr -c
peptide_remd.gro -g peptide_remd.log -e peptide_remd.edr
you probably need to use mpirun here:
mpirun -c 4 mdrun etc.
After I submit mdrun to our cluster, I find the gromacs.e message gives
me this error:
"run input file peptide0.tpr was made for 4 nodes, while mdrun_mpi
expected it to be for 1 node."
It would seem as though I'm doing something wrong in specifying the
number of nodes in the mpi file, but I've checked this over several
times and I can't find anything in the mpi file to suggest that it's
expecting one node. Furthermore, I tried running the simulation without
the "replex" command, and everthing worked just fine for a normal md run
at one temperature with the same mdrun_mpi file.
Do you have any suggestions as to what is going wrong? Am I
submitting the REMD commands correctly?
Thanks,
Max Macaluso
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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