[gmx-users] Radial distance restraints

[David van der Spoel]

Bob Johnson wrote:
> Hello everyone,
> Is there any way to use radial distance restraints? For example, my system is
> cylindrically symmetric (it's a carbon nanotube) and I would like to restrain
> molecules to a certain distance away from the nanotube axis. Obviously, I don't
> care if they the slide along the z-axis or change their orientation with respect
> to the nanotube surface. That is why only radial constraints (sqrt(x^2 + y^2) =
> constant) will work. Any way to do this?
> Thanks,
> Bob Johnson
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you can have position restraints in x and y but not in z direction, this 
will always yield a force obviously. maybe we should implement a 
position restraint with a flat bottom as well (as in distance restraint 
potential).

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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