[gmx-developers] angle restraints
dmobley at gmail.com
Fri Mar 24 16:32:50 CET 2006
> g_angle has the same problem.
> If I am not wrong it only outpus angles between 0 and 180.
> It uses the cosine (inner product of two vectors).
Right. Sorry, I was a bit confused when I wrote earlier, I did look at
this before and that's correct. They are on 0 to 180. I should have
thought of that before.
However, it still seems like it should be possible to do what I'm
suggesting. In particular, on page 64 of the 3.2 manual, it states
that the angle used in angle restraints is using the arccos of a
certain dot product. If this is done correctly in the code, the sign
of the angle will be different depending on whether the vectors are \|
or /|. If you're right and PBC messes this up, then the documentation
is, I suppose, incorrect, since it would mean that the sign of the
angle isn't at all meaningful.
Maybe this could be solved in some (most?) cases by always using a
minimum image convention for computing these angles? (Is there an easy
way to do that?) Then even if one of the vectors moves through PBC, it
will be wrapped back to where it ought to be for the purposes of
computing the angle.
Again, I'm not particularly attached to doing this with angle
restraints if there is some other way to do it. But I desperately need
a way to rotate the angle between a small molecule and a protein
through 360^o, and so far I haven't been able to come up with any
other way to do it. I tried it using the existing angle restraints,
but the orientation gets stuck at the force zeros and I can never push
it through 360^o.
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