[gmx-users] How to resolve Inconsistent moves, Graphene sheet simulation with Gromacs 5.1.4

[Edwine Tendong]

Dear Gromacs users,
 I am new to gromacs and I am trying to simulate a graphene sheet in vacuum
using gromacs 5.1.4. My sheet contains 216 atoms and I have followed the
tips at
 http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
to construct my topology. I made sure my box was periodic​​ and I used the
following X2top command:
gmx x2top -f gra.gro -o gra.top -ff graphene -name GRA -pbc -noparam

This generates 324 bonds, 648 angles as it should. I corrected the dihedral
function to 3, added periodic_molecules = yes and pbc = xyz to my mdp file.

My  simulation runs fine but mdrun reports "There were 44 inconsistent
shifts. Check your topology"  at the end of the run. I am not using
pressure coupling.

Here are my topology  mdp and coordinates:
https://www.dropbox.com/s/qgdmgeo3uyrs099/gra.top?dl=0
https://www.dropbox.com/s/782cwo5uf2a7ozg/gra.gro?dl=0
https://www.dropbox.com/s/ymazo1p90kt9zu4/md.mdp?dl=0

I have been unable to determine the source of this error even after going
through many posts in the mailing list. If someone can take a look at these
simulation files and point me in the right direction then I will be very
grateful.
Thanks a lot in advance.


-- 
Edwine TENDONG
edwine.tendong at aims-cameroon.org
M.Sc Condensed Matter Physics
African Institute for Mathematical Sciences
P.O Box 608, Limbe, Cameroon
Tel (mob.): (+237) 677-162-446