[gmx-users] how to submit replica exchange MD simulation

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 9 14:23:16 CEST 2007

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 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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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