# RE: NAMD-L: question about harmonic constraints

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Wed Apr 12 2006 - 11:25:23 CDT

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

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