[gmx-users] Radial distance restraints

David van der Spoel spoel at xray.bmc.uu.se
Thu Apr 13 22:15:14 CEST 2006

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 

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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