RE: NAMD-L: question about harmonic constraints

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Wed Apr 12 2006 - 13:31:20 CDT

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

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