[gmx-users] Bugs in gromacs 4

Jelger Risselada H.J.risselada at rug.nl
Wed Nov 26 15:32:25 CET 2008

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 

1) There is never memory allocated for the pointers to the user defined 

mdatoms->cU1 etc.

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 

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.




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