[gmx-users] 1-4 interaction between atoms in PBC mode

[Darrell Koskinen]

Dear GROMACS-ians,
I have created an infinite graphene sheet and upon running grompp, I get 
the following response:

/Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 
which is larger than the 1-4 table size 1.000 nm
Warning: 1-4 interaction between 9244 and 9963 at distance 19.553 which 
is larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
These are ignored for the rest of the simulation/

I assume that atoms from opposite ends of the simulation box are being 
seen by GROMACS as being 1-4 neighbors as a result of the PBC, but the 
shortest distance between the atoms is not being observed. Is this the 
problem? Is this problem resulting in the system exploding? And, how do 
I resolve this problem?

Thanks.

Darrell