[gmx-developers] bug in 407 with charge groups

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 2 15:03:15 CET 2010

On 2010-11-02 14.09, David van der Spoel wrote:
> 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.


Charge groups of > 32 atoms will silently give the wrong result. Shall I 
put back the fatal error that used to exist in grompp?

In that case we need to release 4.0.8 (and possibly 3.3.5 as well?).

>> 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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