[gmx-developers] PosRes development: Include cylindrical constraints?

Jochen Hub jhub at gwdg.de
Wed Jan 9 13:42:19 CET 2008

Dear developers,

I read about your plans to implement posisiton restraints with a 
flat-bottomed potential:


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(x^2+y^2) - r0)^2 * H( \sqrt(x^2+y^2) - 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 

So, this may be something to keep in mind when extending the posres code.

Cheers from Goettingen,

Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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