Question about Tcl/customising the colvar module

Date: Tue May 25 2010 - 04:25:34 CDT

Dear developers and all,
 I'm seeking to constrain the rotational motion around the z-axis, specifically
for a center-of-mass coordinate of my protein. We've been working in this
coordinate for translational modes. (Background: This protein of interest is
bound to a membrane protein, and its dynamics have shown some important
characteristics depending on its orientation.)

 Having read the capabilities of the tcl-forces module, I think a tcl-script
would have a lot of slow-down tracking the number of atom-groups and assigning
respective torques on ~30 residues. So, I'm thinking of basing this angular
coordinate within the colvars module.

 Are the developers working on something similar in this regard? I believe that
the orientation module is analogous in purpose, but I wish to keep other
angular degrees of freedom "free". If not, where might I begin looking for help
on writing my own colvars (e.g. documentation)? At the moment, I'm figuring out
whether I can decompose the optimal quaternion returned by orientation and
decomposing it into a rotation in Z, followed by rotation in the other two
non-relevant degrees.


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