[gmx-users] Orientation restraints

Bob Johnson robertjo at physics.upenn.edu
Tue Apr 11 20:58:30 CEST 2006

Hello everyone,
My system consists of DNA and a carbon nanotube. I would like to restrain the
DNA bases in a way that the plane formed by each base is parallel to the
z-axis. In other words, I would like to orient the bases such that the normal
of each plane is perpendicular to the z-axis. I don't think using angle
restraints is sufficient for what I want to do because there you can only
restrain pairs of atoms. Any ideas how I could define a normal vector to each
plane and have that maintain a 90 degree angle with respect to the z-axis?
Bob Johnson

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