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

Jochen Hub jhub at gwdg.de
Thu Jan 10 16:07:51 CET 2008

p.s.: Would you agree if I add a little comment on that issue to the 
respective wiki-page?


Jochen Hub wrote:
> Dear developers,
> I read about your plans to implement posisiton restraints with a 
> flat-bottomed potential:
> http://wiki.gromacs.org/index.php/Position_Restraints_Development
> 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 membrane).
> So, this may be something to keep in mind when extending the posres code.
> Cheers from Goettingen,
> Jochen

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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