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

[Jochen Hub]

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

-- 
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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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