Extend flat-bottom position restraints
I received a request from another group to implement the cylindrical position restraints along x and y. The current code assumes the cylinder is aligned along z. The code changes should be fairly minimal, and this would be a useful feature as the planar geometry already allows for planes perpendicular to any axis.
Added flat-bottom cylindrical restraints in x and y.
The code previously only allowed the long axis of the cylinder
to be aligned along z. This patch allows the cylinder to be
aligned along any axis.
Old topologies and .tpr files will still work for all geometries with
g values from 2 to 5, as 2 is now just a synonym for a z-directional
cylinder. The new values are g=6 for x, g=7 for y, and g=8 for z.
The manual has been updated to reflect these changes.
Introduced a new static function that computes forces and energy for the