[gmx-developers] angle restraints

David Mobley dmobley at gmail.com
Thu Mar 23 18:19:37 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

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