[gmx-users] REMD - subsystems not compatible

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 24 16:52:09 CEST 2019


Generally the REMD code has written some analysis to the log file above
this error message that should provide context.

More generally, you can use gmx check to compare the .tpr files and observe
that the differences between them are only what you expect.


On Wed, 24 Apr 2019 at 15:28, Per Larsson <larsson.r.per at gmail.com> wrote:

> Hi gmx-users,
> I am trying to start a replica exchange simulation of a model peptide in
> water, but can’t get it to run properly.
> I have limited experience with REMD, so I thought I’d ask here for all the
> rookie mistakes it is possible to do.
> I have also seen the earlier discussions about the error message, but
> those seemed to be related to restarts and/or continuations, rather than
> not being able to run at all.
> My gromacs version is 2016 (for compatibility reasons), and the exact
> error message I get is this:
> -------------------------------------------------------
> Program:     gmx mdrun, version 2016.5
> Source file: src/gromacs/mdlib/main.cpp (line 115)
> MPI rank:    32 (out of 62)
> Fatal error:
> The 62 subsystems are not compatible
> I followed Marks tutorial on the gromacs website and have a small
> bash-script that loops over all desired temperatures, run equilibration
> etc.
> I then start the simulation like this:
> $MPIRUN $GMX mdrun $ntmpi -ntomp $ntomp -deffnm sim -replex 500 -multidir
> ~pfs/ferring/gnrh_aa/dipep_remd/sim*
> What could be the source of this incompatibility?
> Many thanks
> /Per
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