[gmx-users] 1-4 interaction between atoms in PBC mode
darrellk at ece.ubc.ca
Tue Sep 22 06:33:00 CEST 2009
I did not have the statement "periodic_molecules = yes" in the .mdp
files. I only had the statement "pbc=xyz" in the .mdp files.
So, I added the "periodic_molecules = yes" statement to the .mdp files
and ran the simulation again. However, this did not appear to resolve
the problem as I received the same warning.
> Date: Mon, 21 Sep 2009 16:56:48 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4AB723B0.6040708 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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?
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