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.
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