[gmx-users] sum of largest charge group radii

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 28 13:59:24 CET 2011

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.


> 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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