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 <[email protected]>
Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
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 <[email protected]>
>> Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode
>> To: Discussion list for GROMACS users <[email protected]>
>> Message-ID: <[email protected]>
>> 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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