[gmx-developers] bug in 407 with charge groups

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 2 14:09:13 CET 2010

On 2010-11-02 13.45, Berk Hess wrote:
> Have you checked if the bug is really gone in 4.5.x?
> 4.5 has all-vs-all loops, which are used by default (thus no neighbor
> searching).
> Could you try to run with GMX_NO_ALLVSALL?
Good point. The bug is still there.
I will file a bugzilla.
> Thanks,
> Berk
> On 11/02/2010 01:31 PM, David van der Spoel wrote:
>> A local user here brought to my attention that in 4.0.7 there is a
>> serious bug due to charge groups. If you have a small molecule with
>> all atoms in one charge group and infinite cutoffs in vacuo the energy
>> is wrong. If you put each atom in it's own charge group the result is
>> correct (as compared to Macromodel). The reason appears to be that the
>> neighborlist is incorrect:
>> 1 cg/molecule
>> <   Coulomb + LJ                       0.000569           0.022    29.0
>> 1 cg/atom
>>>   Coulomb + LJ                       0.000620           0.024    24.9
>> in other words, 51 interactions are left out. In 4.5.x this bug is no
>> longer there, so it would be good if the fix that went into 4.0.x as
>> well. I can't seem to find any notion of this being fixed in the git
>> logs of ns.c though.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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