Talk:Position Restraints Development

From wiki.gromacs.org

It may be of interest to implement this potential in way such that it allows to employ a cylinder-like potential:

V(x,y,z) = 0.5*k*( \sqrt(x2+y2) - r0)2 * H( \sqrt(x2+y2) - r0)

where H is the heaviside step funktion and r0 the radius of the cylinder. This would be a kind of flat-bottomed potential, which, however, only applies in the x-y-plane. Such potentials are useful for computing PMFs for permeation through membrane channels since they allow to have a well-defined area per channel (or channel density in the membrane).

I would suggest to add 3 new mdp option, such as posres_grps, posres_r0 and posres_direction. In posres_grps one could define groups which are subject to some flat-bottom posres potential. The width of the flat bottom would be defined in posres_r0. posres_disrection could allow options such as xyz, xy, x, y, or z which would refer to:

• xyz : sphere-like flat-bottom potential

• xy: cylinder-like flat-bottom potential

• x, y, or z, layer-like flat-bottom potential in x-,y-, or z-direction

Such an implementation would be quite straight-forward, I guess. To allow posres_r0 to change within an FEP run one could allow to give two posres_r0 values per posres-group.

Any suggestions? Agreement?