From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Apr 20 2016 - 13:51:43 CDT
Hi Giulia, rotation decomposition is currently implemented by a spinAngle
colvar component. To test it in VMD, feel free to use the following Tcl
script to visualize the total rotation axis and angle, and compare them to
the angles of sub-rotations:
https://github.com/colvars/colvars/blob/master/colvartools/colvar_display.tcl
The display commands won't work in NAMD, of course.
Also, you may want to try an alpha version of VMD because 1.9.2 does not
let you define variables using more than one configuration files due to a
bug, which was later fixed.
Giacomo
On Wed, Apr 20, 2016 at 1:25 PM, giulia palermo <giulia.palermo83_at_gmail.com>
wrote:
> Dear all,
>
> I would like to calculate the rotation angle of one specific protein
> domain around one axis.
> Is is possible with TCL scripting?
>
> I can calculate the principal axes of inertia and the X, Y, Z components.
> But , how can I calculate the rotation of the domain around, as
> example, the component Z?
>
>
> Thank you very much
>
> Giulia
>
>
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
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