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

[Justin A. Lemkul]

Mark Abraham wrote:
> 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.
> 

In the 3.x series, the option to use is "pbc = full," but as Mark suggests, 
upgrading to 4.0.5 is probably a better idea.

-Justin

> 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
>>>> >>       
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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