[gmx-developers] angle restraints

hessb at mpip-mainz.mpg.de hessb at mpip-mainz.mpg.de
Fri Mar 24 14:45:25 CET 2006

> Dear developers,
> I need to compute the PMF for rotating an angle (in particular, the angle
> between two atoms in a small molecule and a reference atom in a protein),
> and I've been trying to do this using the existing angle restraints code,
> but it isn't working well for me since angle restraints (unlike distance
> and
> dihedral restraints) currently use a functional form that involves a
> cosine
> rather than simple harmonic angle restraints. This means that the force
> has
> more than one zero and sometimes the angle I'm restraining can end up
> trapped at the alternate zero of the force (the one OPPOSITE the one I'm
> restraining to).
> Anyway, I wanted to inquire whether any of the developers would be
> interested in adding an alternate angle restraint type, perhaps type "2",
> which would use simple harmonic restraints (like, for example, the
> dihedral
> restraints), as I can imagine this would be useful to others, and should
> be
> relatively straightforward. I am willing to help test it.
> Alternatively, I suppose, I can just implement it in my own code. Or I can
> do so and when I get it working I can share with others. But it seemed
> like
> it might make more sense to have it put into GROMACS itself, as I can't
> imagine I'm the only one who ever wants to have simple harmonic angle
> restraints.

I think this case is not defined so uniquely.
I assume you want to distinguish \| from /|.
But is the angle \| equal to |/ (rotated system)?
And \| with one vector moved through pbc is | \.
So with the definition I assume you would like
to have the angle depends on the distance between
the vectors and the sign will change when the shortest
distance between the vectors switches pbc.


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