Re: Question about Tcl/customising the colvar module

From: Patrick Yee (pyee_at_nd.edu)
Date: Tue May 25 2010 - 18:47:35 CDT

Giacomo,

Would you mind telling me the new colvars you are considering adding?
These might be very useful for my research in the future.

Thank you,

Pat

On 5/25/10, Giacomo Fiorin <giacomo.fiorin_at_temple.edu> wrote:
> 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.
>
> Giacomo
>
> ---- ----
> Dr. Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science - Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> giacomo.fiorin_at_temple.edu
> ---- ----
>
>
>
>
> 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
> 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.
> >
> >
>
>

-- 
Pat Yee - ChEg 2011
Vice President of Am. Inst. of Chemical Engineers at ND
Director of Interview Preparation for ND Consulting Consortium

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