Re: Applying SMD to a domain of protein

From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Fri Feb 01 2008 - 11:13:58 CST

Hi Monika,
 Only easy solution to apply user-defined forces in NAMD is to use
TCL-FORCES tutorial. Type in google: "force tutorial in namd " and you can
download the pdf in the first link and learn how to be very sophisticated in
applying forces........you can also fnd the same tutorial in TUTORIAL
section on NAMD official website. I hope it helps.

-harish

On Feb 1, 2008 1:49 AM, Monika <mon_sharma_at_research.iiit.ac.in> wrote:

> Dear All,
> I have a two-domain protein. I wish to apply SMD to one of domain for
> viewing hinge movement. I am facing problems in locating the direction
> of movement. By this I mean how to calculate the direction of movement,
> using vectors formulation. In tutorials, I could find the application to
> one atom, so the job becomes pretty much simpler. Here I want to move
> the whole domain. Is it possible to do, or i am just speculating more
> with SMD? Second thing, how to go for direction calculations applied to
> whole domain?
> All suggestions are welcome.
> Thanks in advance.
> Regards,
> Monika
>
>
>
>

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