[gmx-users] Creating an infinite sheet of graphene

#TAN BENG HAU IAN# BTAN023 at e.ntu.edu.sg
Thu Aug 29 11:28:39 CEST 2013

Dear all,

I am trying to simulate a graphene sheet, periodic in xy. I am using Gromacs 4.5.5. My simulation fails before I can complete an energy minimisation in mdrun.

For the force field I added the following lines to  atomname2type.n2t of a copy of oplsaa.ff
3 C opls_145 0.0 12.011 3 C 0.140 C 0.140 C 0.140
4 C opls_145 0.0 12.011 2 C 0.140 C 0.140

For the structure preparation I used Atomic Simulation Environment python library ase.structure to create a sheet that is 17.04 nm by 9.38048587 nm (this is the exact precision provided by ase).

After this I used g_xtop to create the topology.
g_x2top -f graphene.gro -o cnt.top -name GRA -pbc

I also used editconf to center the graphene sheet in a box that is 17.04 nm by 9.38048587 nm by 20 nm.

The mdp file for the energy minimisation is as follows

integrator      = steep         ; Algorithm (steep = steepest descent minimization)
emtol           = 1000.0        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps          = 50000         ; Maximum number of (minimization) steps to perform
nstlist         = 1             ; Frequency to update the neighbor list and long range forces
ns_type         = grid          ; Method to determine neighbor list (simple, grid)
rlist           = 1.0           ; Cut-off for making neighbor list (short range forces)
coulombtype     = PME           ; Treatment of long range electrostatic interactions
rcoulomb        = 1.0           ; Short-range electrostatic cut-off
rvdw            = 1.0           ; Short-range Van der Waals cut-off
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
periodic_molecules = yes

I was able to run x2top and grompp successfully. With mdrun, I receive the error

Warning: 1-4 interaction between 5761 and 5918 at distance 16.685 which is larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding, ....

I have checked both atoms 5761 and 5918 and they lie right on the edge of the box (the graphene sheet is orientated in the xz axis):
C 5761 0.799 10.000 0.071
C 5918 0.922 10.000 16.898

It seems like there is a problem with the periodicity. Have I defined a box that is too small? I appreciate any assistance.

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