Re: Question about Tcl/customising the colvar module

From: Giacomo Fiorin (
Date: Tue May 25 2010 - 08:54:17 CDT

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, <> 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 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.
> Thanks,
> Poker.

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