Re: [AMBER] Need help with MMPBSA.MPI

From: Bill Miller III <>
Date: Mon, 16 Apr 2012 12:21:59 -0400

Unfortunately, the calculation must be restarted from the beginning if one
or more threads ended unexpectedly. The restart files that are created are
used during the calculations, and are not actually restart files used to
restart the calculation.

Also, will merge all the results in the end to make the final
output file.


On Mon, Apr 16, 2012 at 12:12 PM, Victor Ma <>wrote:

> hi
> I'm doing energy decomposition in mmpbsa. Since it's really slow running in
> serial, so I'm doing the calculation with MMPBSA.MPI on 24 nodes. HOwever,
> among the 24 parallel jobs, a few of them terminated unexpectedly. Is there
> anyway to rescue the calculation instead of starting from scratch again? I
> imagine I could try something like this:
> mpiexec_ssh -np 24 MMPBSA.MPI -O -i _MMPBSA_pb_decomp_com.mdin -o
> _MMPBSA_complex_pb.mdout.1 -sp complex_wat.prm -cp complex_new.prm -rp
> receptor.prm -lp lig.prm -y _MMPBSA_complex.mdcrd.1 -r _MMPBSA_.restrt.1
> Or since there is a restart file "_MMPBSA_.restrt.1", can I resume the
> calculation?
> Also how do i merge all these separate calculations in the end? Thanks!!
> Best,
> Victor
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Apr 16 2012 - 09:30:04 PDT
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