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

[darrellk at ece.ubc.ca]

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?

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
>
>========================================