[gmx-users] Orientation restraints

[Mark Abraham]

Bob Johnson wrote:
> 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?

Using multiple angle restraints for the atoms in the plane to the Z-axis 
will do the job fine. There will already be improper dihedral potentials 
that are keeping the aromatic rings planar, so you won't need to be too 
zealous here. Maybe one or two pairs of atoms per ring and the rest 
should fall into line just fine. Test it out, obviously!

Mark