[gmx-users] how to submit replica exchange MD simulation
njmm2 at cam.ac.uk
Mon Apr 9 13:20:09 CEST 2007
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
grompp -f PME1.mdp -po PME1out.mdp -c peptide.gro -p peptide.top -o
peptide1.tpr -np 4
grompp -f PME2.mdp -po PME2out.mdp -c peptide.gro -p peptide.top -o
peptide2.tpr -np 4
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
After I submit mdrun to our cluster, I find the gromacs.e message gives me
"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?
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