Hello Jakob--
>
> I wish to use angles constaints constraining three atoms, which are
> not related by bonds, to a certain angle. It seems it is only
> possible to constrain dihedral angles, and guess adding to the
> parameter file is not a good option.
>
If you group three atoms together in a rigid body (using the group()
method of the IVM) the angle will be preserved. Some care must be
taken if you are also using torsion angle dynamics and the atoms are
involved with bonds to other atoms. It is also possible to write a
simple Python energy term using bondAngle.BondAngle if you'd like a few
angle-only restraints If things aren't 100% clear please provide
further details.
best regards--
Charles
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Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
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