[gmx-users] Bugs in gromacs 4

[Jochen Hub]

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

> 
> 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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-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************