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

[Mark Abraham]

Darrell Koskinen wrote:
> 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.

One error was not mentioning your GROMACS version. :-) Your grompp 
command line above is for some 3.x version, not some 4.x version. 
periodic_molecules is a 4.x feature (but mentioned only in section 7.3 
IIRC). I've no idea how to solve your problem for 3.x, but if you can 
reasonably upgrade, you should.

Mark

> 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
>>> >>       
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>