[gmx-users] sum of largest charge group radii

[Gavin Melaugh]

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?

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
>>>>>>
>>>>
>>
>>
>