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

[Mark Abraham]

Darrell Koskinen wrote:
> 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.

Well that's a pretty basic requirement that you needed to satisfy. 
Obviously you also need to re-generate your .tpr from the new .mdp. 
That'd be the most likely reason for an *identical* output.

Have you done enough background reading (e.g. wiki page on Carbon 
Nanotube simulations) and/or gotten some experience with normal GROMACS 
simulations?

Mark

>> 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
>>   
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