[gmx-users] sum of largest charge group radii

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 28 14:09:26 CET 2011

Gavin Melaugh wrote:
> Yeah I did that and there was no error, cheers. I did the same thing a
> week a go for a united atom model of hexane, I did not get the warning
> then even though the molecules were still broken. Peculiar?

Then there must be differences in the way the charge groups are set up.  For a 
UA hexane, it shouldn't matter how you set it up (since all the UA atoms are 
probably uncharged, anyway), but for an AA model, it will matter.


> Justin A. Lemkul wrote:
>> Gavin Melaugh wrote:
>>> Then is this a bug?, or do I have to have a box in which all the
>>> molecules are whole. Does that not defeat the purpose of having a
>>> periodic box?
>> In a sense, maybe this is a grompp bug, in that it does not account
>> for periodicity.  There is no harm in using this run input file,
>> though, which you can verify by making the molecules whole and then
>> re-running grompp.  You shouldn't see the same error.
>> -Justin
>>> Gavin
>>> Justin A. Lemkul wrote:
>>>> Gavin Melaugh wrote:
>>>>> Hi Justin
>>>>> By "broken" do you mean split at the edge of the periodic box? If so
>>>>> then yes.
>>>> Then that's your problem.
>>>> -Justin
>>>>> Gavin
>>>>> Justin A. Lemkul wrote:
>>>>>> Gavin Melaugh wrote:
>>>>>>> Hi
>>>>>>> I have installed the new version of gromacs and so far I only use
>>>>>>> it as
>>>>>>> a check when running grompp as it gnerates more information about
>>>>>>> cut
>>>>>>> off charge group radii etc.
>>>>>>> For a system of 256 hexane molecules in a cubic box I get the
>>>>>>> following
>>>>>>> error.
>>>>>>> WARNING 1 [file pbc.mdp]:
>>>>>>>   The sum of the two largest charge group radii (5.231524) is larger
>>>>>>> than
>>>>>>>   rlist (1.700000)
>>>>>>> This doesn't even make sense since my as system itself fits in a
>>>>>>> 3.2 nm
>>>>>>> cubic box. I am pretty sure my topology is correct. I have seen
>>>>>>> on the
>>>>>>> mailing list that there have been problems with this but they
>>>>>>> have all
>>>>>>> been for bigger molecules.
>>>>>> Are any of the molecules broken?  That was the exact case just a
>>>>>> couple of days ago:
>>>>>> http://lists.gromacs.org/pipermail/gmx-users/2011-January/057980.html
>>>>>> -Justin
>>>>>>> Gavin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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