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

Omer Markovitch omermar at gmail.com
Mon Sep 21 09:21:20 CEST 2009

> 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,

Are you sure? have you looked at the last "good" frame before this message?
GMX treats PBC as it should during MD neighbour search, so maybe this is a
pair that was initially close and interacting, but later moved away from
each other.

> 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?
If you are sure that everything else is ok, then extend the table extension.
Two other things to work around this are either reduce timestep or check
that your definition of the box is as it should.
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