[gmx-users] sum of largest charge group radii

[Gavin Melaugh]

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?

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
>>>>
>>
>>
>