[gmx-developers] bug in 407 with charge groups

Berk Hess hess at cbr.su.se
Tue Nov 2 13:45:33 CET 2010

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
Could you try to run with GMX_NO_ALLVSALL?



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.

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