Hi Omer,
The atoms in question are part of a graphene sheet and are located at
two opposite ends of the box. They should not move as they are bound
inside the graphene sheet. The initial separation between these atoms is
19.678 nm, which is the same distance as in the warning message. So the
position of these two atoms apparently does not change from the
beginning of the simulation until the point at which the warning occurs.
Darrell
Date: Mon, 21 Sep 2009 10:21:20 +0300
From: Omer Markovitch <omer...@gmail.com>
Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
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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.
--Omer.
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