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

Alex nedomacho at gmail.com
Sun Apr 22 01:39:16 CEST 2018


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    
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 
(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.


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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