[gmx-users] Re: Implementing Radial Distance Constraints

Bob Johnson robertjo at physics.upenn.edu
Mon Apr 17 23:20:05 CEST 2006

>please be more clear.
>if we assume your cnt is centered along the z-axis, given roughly by
>x^2+y^2 = d0. Am I correct in assuming that you want all other particles
>to have x^2+y^2 <= d1, where d1 < d0 ?

The molecules in my system adsorb to the tube's outer wall. They are not inside 
the tube. Typically, the adsorbates reside 3.5A above the nanotubes surface (a
typical distance for molecules interacting via VdW with an aromatic molecule).
I want to constrain molecules to always adopt a monolayer about the nanotube.
Therefore, I want to put a constraint on certain atoms to reside 3.5A above the
nanotube. Let's say my nanotube has a radius of 0.5A. I would then want to
implement a potential given by V = 1/2 k (R-0.5A)^2 where R = sqrt(x^2+y^2).
This way, the atoms are able to slide along the z and cirumferential


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