[gmx-developers] bug in 407 with charge groups

[Berk Hess]

On 11/02/2010 04:18 PM, David van der Spoel wrote:
> 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.
>
Are you sure exactly 32 works fine and the limit is not 31?
Then I will change the limit in forcerec.h.
That check is even more important, since that is in mdrun where the
actual limitation is.

Berk
>
>> 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.
>>>>>
>>>>
>>>>
>>>
>>>
>>
>
>