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

[Mark Abraham]

Darrell Koskinen wrote:
> 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?

Did you use periodic_molecules = yes in your .mdp file?

Mark