# RE: NAMD-L: question about harmonic constraints

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Apr 12 2006 - 17:05:24 CDT

Hi Margaret!

I'm curious. Could you please send us the script, so I could use it, too?
(as I don't know Peter :-))

Thanks,

Gianluca

On Wed, 12 Apr 2006, Margaret Shun Cheung wrote:

>
> Dear JC and NAMD users,
> This is a followup about how to transform an axis of a molecule to (0,0,z).
> Peter at VMD-L has sent me a tk script to do that, and it worked.
> Thank you!
> Sincerely,
> Margaret
>
> On Wed, 12 Apr 2006, Margaret Shun Cheung wrote:
>
> >
> > Dear JC and NAMD users,
> > Thank you very much for your explanation. After trying for quite a while,
> > I embarrassingly admit that my limited scripting skills fail to
> > transform/3D-rotate my molecule so that its long rotational axis can be
> > aligned to (0,0,z).
> > Could you please show me how to do this with NAMD or VMD? Or is it a script
> > available before I start re-inventing
> > the wheels (probably not even do it correctly...)?
> > Thank you very much.
> > Sincerely,
> > Margaret
> >
> > On Tue, 11 Apr 2006, JC Gumbart wrote:
> >
> > > That's a good question.
> > >
> > > If you look at the formula (see
> > > http://www.ks.uiuc.edu/Research/namd/2.6b1/ug/node32.html), with v = 0,
> > > you
> > > get the potential to be U = 1/2k[(R-R0) dot n]^2. Ignoring R0 (assume
> > > it's
> > > zero), this becomes U = 1/2k[Rx*nx+Ry*ny+Rz*nz]^2. So, if your
> > > constrained
> > > atoms drift along a direction such that the sum is zero, you will have no
> > > applied force! This is avoided though by the vector n only having one
> > > component.
> > >
> > > I actually figured this out after running into my own problem with using
> > > SMD
> > > to constrain something. I was initially shocked to see atoms I thought
> > > were
> > > constrained moving very freely, but now I understand why, and how to get
> > > around it.
> > >
> > >
> > > -----Original Message-----
> > > From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> > > Of Margaret Shun Cheung
> > > Sent: Tuesday, April 11, 2006 9:07 PM
> > > To: JC Gumbart
> > > Cc: namd-l_at_ks.uiuc.edu
> > > Subject: Re: namd-l: NAMD-L: question about harmonic constraints
> > >
> > > 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
> > > (\$f1x,\$f1y,\$flz).
> > >
> > > 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!
> > > Sincerely,
> > > Margaret
> > >
> > >
> > > 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 http://glue.umd.edu/~mscheung
> > > College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> > > ------------------------------------------------------------
> > >
> > >
> >
> > 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 http://glue.umd.edu/~mscheung
> > College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> > ------------------------------------------------------------
> >
>
> 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 http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------
>
>

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
+1 (206) 685 4432
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:31 CST