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

[Darrell Koskinen]

Hi Mark,
Yes, I have had success running many GROMACS simulations with a simple graphene sheet inside a box. 

I believe I have regenerated the .tpr file from the new .mdp as the very first command I issue is:
grompp -np $NUM_PROCS  -f em.mdp -c $GRO_FILE -p $TOP_FILE -o emtopol.tpr -n index.ndx

Please advise me on what I may be doing wrong.

Also, note that there appears to be no reference to the statement "periodic_molecules = yes" in the GROMACS manual as I did a search in the manual for  "periodic_molecules" and the search came back empty.

Thanks.

Darrell

Date: Tue, 22 Sep 2009 15:07:03 +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: <4AB85B77.10505 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

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
>> >>   
>>