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

[Justin A. Lemkul]

darrellk at ece.ubc.ca wrote:
> Hi Justin,
> I am using version 3.3.3 and read through the version 3.3 manual but do
> not see an option to set "pbc = full" in this manual. I only see
> options to set pbc to "xyz" or "no". Will setting pbc=full be
> recognized in GROAMCS version 3.3.3 and will this solve my problem?
> 

Yes, it will.  I don't know why it was never in the documetation.

-Justin

> Thanks.
> 
> Darrell
> 
>> Date: Tue, 22 Sep 2009 06:45:13 -0400
>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> 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: <4AB8AAB9.7010906 at vt.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>>
>> 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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-- 
========================================

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

========================================