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

Edwine Tendong edwinasaba at gmail.com
Sun Apr 22 12:48:19 CEST 2018

Greetings Alex,

Thanks for your prompt reply and suggestions. I used the parameters you
suggested in my itp file. Here is my itp file

I prepared my graphene sheet in VMD using the C-C bond length = 0.142nm and
made sure the box size respected periodicity (My sheet is rectangular:
2.5560000   2.214000 ). Here is a visualisation of the box and its periodic
images in vmd

I then generated the topology with x2top version 5.1.4 with the command
''gmx x2top -f gra.gro -o gra.top -ff graphene -name GRA -pbc -noparam''
There are  324 proper dihedrals,    0 impropers,  648 angles     972
pairs,   324 bonds and   216 atoms. The connectivity looks good. x2top
automatically assigns the dihedral type 1 so I manually change to type 3 to
match the supplied dihedral energies you suggested.
Then doing the run  with the command
gmx grompp -f md.mdp -c gra.gro -p gra.top -o md_01.tpr
gmx mdrun -v -deffnm md_01

Reading file md_01.tpr, VERSION 5.1.4 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1

Using 1 MPI thread
Using 8 OpenMP threads

starting mdrun 'GRA'
100000 steps,    100.0 ps.
step 99900, remaining wall clock time:     0 s
Writing final coordinates.
There were 44 inconsistent shifts. Check your topology
step 100000, remaining wall clock time:     0 s

I have visualised the trajectory and the atoms just vibrate about
equilibrium as expected. Also removing dihedral does not help.
I will be very grateful for any further suggestions as I need this to work


On Sun, Apr 22, 2018 at 5:09 AM, Alex <nedomacho at gmail.com> wrote:

> Hi,
> Your mdp file contains all the necessary things for this simulation to
> proceed normally, i.e. COM motion is removed, periodic molecules are set
> and full pbc is all there. Visualize the trajectory and see what is going
> on. "I corrected the dihedral function to 3" makes no sense, sorry. The
> type of dihedrals must correspond to what it was wherever you found the
> dihedral energy term.
> For graphene, the symmetry is incredibly simple, let's try to use my
> parameters. I happen to think that the graphene situation for Gromacs is
> hopeless, because so many people seem to get their parameters from very
> strange places, including out-of-the-box stuff from FFs like OPLS-AA.
> 1. Remove all dihedrals from your topology.
> 2. Make sure your box size corresponds exactly to the lattice constant.
> For graphene, it is a=2.46 A and the bond length is a/sqrt(3). In Gromacs,
> for the bulk bonds I use (CJ is my bulk graphene carbon): CJ    CJ
> 1    0.14200   420420.0
> 3. The angle that works for me is: CJ     CJ     CJ      1 120.000
> 659.346
> 4. Test if this works without dihedrals.
> 5. Try adding dihedrals.
> Parameters for dihedral:
> CJ     CJ     CJ     CJ      3     17.30770   0.00000 -17.30770 0.00000
> 0.00000   0.00000
> This absolutely works, provided you have set up your non-bonded parameters
> and nrexcl properly.
> All parameters from http://iopscience.iop.org/arti
> cle/10.1088/0957-4484/25/48/485701/meta (shameless self-plug). Not a
> great paper, but can be useful. The dihedral parameters above need to be
> consistent with the number of dihedrals. If I recall correctly, the paper
> lists ONE dihedral per bond, so count your dihedrals. It is not expected to
> change your results much (unless you're specifically interested in
> ripples), but still try to double-check what the paper says and how your
> topology is set up.
> Alex
> On 4/21/2018 5:15 PM, Edwine Tendong wrote:
>> 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.
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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

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