[gmx-users] membed software inconsistency error

Jason Mast jasonmast at mail.usf.edu
Fri Mar 24 16:56:44 CET 2017

Dear Gromacs Users,

I'm trying to embed a protein into a lipid bilayer using the -membed option
of gmx mdrun. After executing the command:
gmx mdrun -s topol.tpr -deffnm out -membed embed.dat -mp topol.top -mn
I select the groups for the Protein and Lipid_Bilayer when prompted for
them, and then I get an error message:

Program:     gmx mdrun, version 2016
Source file: src/gromacs/topology/mtop_util.cpp (line 249)

Software inconsistency error:
gmx_mtop_atomlookup_settle_init called without settles

I have tried searching online via Google for the meaning and solution to
this error, but all I can find are links to the source code that contains
that method call. Section 6.14 of the Gromacs User Manual doesn't contain
any information to address this error. Additionally this error isn't listed
at www.gromacs.org/Documentation/Errors.

I have tried this with and without the -mp and -mn options, and I receive
the same response. I have checked all of the input files (system.gro,
index.ndx, topol.top, embed.mdp, & embed.dat) for errors, and everything
looks correct.

Before executing mdrun I run gmx grompp and it completes without any
warnings or errors. It produces a few common notes, which I consider to be
okay and not relevant to this error.

Here is a subset of the mdp parameters which could potentially be relevant:
comm-mode   = Linear
comm-grps     = System
cutoff-scheme = group ; Verlet is not yet implemented for use with membed
tcouple           = v-rescale
tc-groups        = Protein Lipid_Bilayer Water
Pcoupl            = no
freezegrps       = Protein
freezedim        = Y Y Y
energygrps       = Protein
energygrp_excl = Protein Protein

I am using the Martini 2.2 coarse grain force field. I have used this force
field for other md simulations without using the membed tool, and this
error was never produced.

Can anyone offer any guidance or pointers about what I could be doing wrong
or otherwise a way work around the error?

Thank you for reading,

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