[gmx-users] Software inconsistency error with version 2016.1

Qasim Pars qasimpars at gmail.com
Fri Jan 27 11:54:47 CET 2017

Dear gmx users,

When I type gmx mdrun -v -deffnm npt, I get the below error in the NPT step
for a few protein-ligand complexes that have the different atom numbers.
But with -nt 16 I don't get it. For instance, the number of atoms in a
system is ~40000. That works with -nt 16 flag (gmx mdrun -v -deffnm npt -nt
I would ask you how can I fix that error and use all cores (32 cores with
hyperthreading) on my machine?
By the way, gmx mdrun -v  npt -ntmpi 4 -ntomp 8 gives the same error.


Program:     gmx mdrun, version 2016.1
Source file: src/gromacs/domdec/domdec_topology.cpp (line 238)
MPI rank:    23 (out of 32)

Software inconsistency error:
Some interactions seem to be assigned multiple times

Any help will be appreciated.

Qasim Pars

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