**From:** Margaret Shun Cheung (*mscheung_at_ipst.umd.edu*)

**Date:** Wed Apr 12 2006 - 17:29:50 CDT

**Next message:**Margaret Shun Cheung: "RE: NAMD-L: question about harmonic constraints"**Previous message:**Gianluca Interlandi: "RE: NAMD-L: question about harmonic constraints"**In reply to:**Gianluca Interlandi: "RE: NAMD-L: question about harmonic constraints"**Next in thread:**Margaret Shun Cheung: "RE: NAMD-L: question about harmonic constraints"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello,

The following was the message from VMD-L, posted by Peter.

If you have questions, please check with the VMD-L

list. :)

Take care.

Margaret

-----

you can do this by using the VMD matrix routines, documented at

http://www.ks.uiuc.edu/Research/vmd/current/ug/node172.html.

For example, for your case, if the long axis of your molecule is along the

vector {a b c}, you can rotate it to align it with the z axis as follows:

set sel [atomselect top all]

set M [transvecinv {a b c}]

$sel move $M

set M [transaxis y -90]

$sel move $M

This performs your task in two steps: transvec inv rotates your vector to

be

along the x axis, and then transaxis rotates about the y axis to align

your

vector with z.

--------------------------------

On Wed, 12 Apr 2006, Gianluca Interlandi wrote:

*> 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.
*

*> -----------------------------------------------------
*

*>
*

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

------------------------------------------------------------

**Next message:**Margaret Shun Cheung: "RE: NAMD-L: question about harmonic constraints"**Previous message:**Gianluca Interlandi: "RE: NAMD-L: question about harmonic constraints"**In reply to:**Gianluca Interlandi: "RE: NAMD-L: question about harmonic constraints"**Next in thread:**Margaret Shun Cheung: "RE: NAMD-L: question about harmonic constraints"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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