[gmx-developers] bug in 407 with charge groups

[David van der Spoel]

On 2010-11-02 16.02, Berk Hess wrote:
> Hi,
>
> There is a MAX_CHARGEGROUP_SIZE defined in forcerec.h.
> This can simply be lowered to 32 (with proper documentation next to 32).
>
The 32 comes from the 32 bit for the t_excl type (unsigned long), 
something completely different in other words. I put hard checks in 
grompp for charge groups of 32 atoms now, this has been committed as well.


> Berk
>
> On 11/02/2010 03:03 PM, David van der Spoel wrote:
>> 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.
>>
>> http://bugzilla.gromacs.org/show_bug.cgi?id=608
>>
>> 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