# RE: NAMD-L: question about harmonic constraints

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Wed Apr 12 2006 - 17:29:50 CDT

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

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

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