[gmx-users] sum of largest charge group radii

[Justin A. Lemkul]

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
>>>
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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