[gmx-users] Bugs in gromacs 4

[Jelger Risselada]

Jochen Hub wrote:
> Jelger Risselada wrote:
>   
>> Finally had a look through the gromacs 4.0 source code.
>> Don't know if this bug/points already have been reported and changed in
>> 4.0.2:
>>
>> 1) There is never memory allocated for the pointers to the user defined
>> groups:
>>
>> mdatoms->cU1 etc.
>>     
>
> I'm not sure, but there is a
>
>     /* The user should fix this */
>     if (FALSE)
>       srenew(md->cU1,md->nalloc);
>     if (FALSE)
>       srenew(md->cU2,md->nalloc);
>
> in ./src/mdlib/mdatom.c.
>
> You can remove the FALSE and get the memory allocation, I guess.
>
> Jochen
>
>   
A hardcoded if(FALSE)  in the middle of no where with the command /*The 
user should fix this */ .
How flexible...... ;-)

greetings

Jelger







>> These pointers will stay NULL when a user defined group is defined in
>> the mdp file.
>> I find these groups normally a pretty useful interface for simple fast
>> implementations.
>>
>> 2) The pull code has indeed completely changed, however to me the
>> questionable factor 0.5 remained the same:
>>   In pull.c:
>>
>> /* Add the pull contribution to the virial */
>>          vir[j][m] += 0.5*f[j]*r_ij[g][m];
>>
>> I do agree with the positive sign of the summation,  but why is there a
>> factor 0.5 to correct for double counting included in the summation. The
>> summation is already ordered as r_ij and f[j] is the distance vector and
>> force between the particle and the equilibrium position of the spring
>> and therefore double counting cannot occur.  Ofcourse it's possible that
>> this factor 0.5 is not meant as a double counting correction factor, but
>> then I don't see where it does come from. If this factor is indeed
>> incorrect it might affect the pressure significantly in case a large
>> pulling group is used.
>>
>> greetings
>>
>> Jelger
>>
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>>     
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