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.abra...@anu.edu.au>
Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4ab85b77.10...@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.abra...@anu.edu.au>
>> Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode
>> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>> Message-ID: <4ab723b0.6040...@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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