COM pulling in geometry cylinder does not conserve energy
The COM pull geometry cylinder uses weighting based on the radial distance with the cylinder reference group. This weighting leads to radial forces. These radial forces are currently ignored (because they are tedious to calculate and they produce inconvenient compression/extension forces). This means that force is not the gradient of the potential and energy is not conserved (although the errors are small for large cylinder radii).
COM pulling options per coord, improved cylinder
The COM pull type (potential/constraint), geometry, dimensions
and pull-start can now be set differently for each pull coordinate.
Also added a flat-bottom potential.
Cylinder geometry now uses a smooth radial weight function and
adds radial forces so it now conserves energy.
There is now also an option for printing the COM of the second group,
as well as the reference value for all pull coordinates.
Writing the distance components to the pull coordinate output is now
optional (off by default).
gmx wham currently only supports input with the old restrictions
(and it checks for this). These restrctions should be removed.