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.
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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