Re: NAMD-L: question about harmonic constraints

From: Margaret Shun Cheung (
Date: Tue Apr 11 2006 - 21:06:33 CDT

Dear JC and NAMD users,

Thank you very much for sharing this clever script. I guess to comply with
the pulling axis, an rotation of the long axis of the aspherical molecule
to align with the pulling axis may be the first step to do. (I sent VMD-L
an email and asked if there are tcl scripts for rotations).

But I am intrigued by the message in which the pulling axis on the
SMDgroup to be only one of
x-, y-, or z- (e.g. (0,0,$flz) ):
it looks like if $fx and $fy can be treated
like $f1z, then the directions of pulling forces for SMDgroup can be

Or is it because of some other reasons that directions of forces coupled
with SMD module should be one of the x-,y-, or z- axis?

Thank you very much!

On Tue, 11 Apr 2006, JC Gumbart wrote:

> The solution to your problem is to use SMD for one part and tcl forces for
> the other.
> For example, you can use SMD to restrain one part of the protein with zero
> velocity along the axis of pulling (please remember, it can only be one axis,
> x, y or z) and then use tcl forces to pull the other part at constant
> velocity.
> I've attached a script I used to pull a small deca-alanine helix in the -z
> direction at constant velocity. I pulled the center of mass of the 10
> C-alpha atoms. This along with the NAMD user guide section on tclforces
> should give you a good start in using it for your purposes.

Margaret S. Cheung,
Ph. D. Postdoctoral Fellow,

Room 2117 Tel: (301) 405-4892
Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
University of Maryland
College Park, MD 20742-2431 email:

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