[gmx-users] sum of largest charge group radii

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Jan 28 13:20:47 CET 2011

Hi Justin

By "broken" do you mean split at the edge of the periodic box? If so
then yes.


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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