On 8/29/13 5:28 AM, #TAN BENG HAU IAN# wrote:
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.
Yes, the box is too small. If it fits the coordinates exactly, there is no room
for the bonds that occur across periodic boundaries. You need to leave a
distance around the whole structure of 1/2 a C-C bond length so that the bonds
can be properly constructed. Otherwise, you just have two carbon atoms directly
on top of one another at each boundary.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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