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

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 10 16:12:58 CET 2008

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

You're also welcome to provide a reference implementation.

> Jochen
> 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

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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