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

[Darrell Koskinen]

Hi Mark,
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.

Please advise.

Darrell
> 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?
>
> Mark
>