Date: Tue May 25 2010 - 22:39:48 CDT
Yes, thank you - that would be excellent to work with.
Quoting Giacomo Fiorin <giacomo.fiorin_at_temple.edu>:
> Hi Poker, we're currently testing (and documenting) new variables that you
> could find useful in this respect. If you're OK to work with this code, I
> can send it to you off-list.
> ---- ----
> Dr. Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science - Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> ---- ----
> On Tue, May 25, 2010 at 5:25 AM, <poker_at_physics.usyd.edu.au> wrote:
> > 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
> > 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
> > 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.
> > Thanks,
> > Poker.
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