VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 18 2007 - 16:51:47 CDT

Oh, I should mention that you should read the source code for the
"imdmenu" plugin which does most of what you need already, in terms of
catching timestep updates and the like.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 18, 2007 at 04:50:16PM -0500, John Stone wrote:
>
> Hi,
> As I recall, you can query the "ufx", "ufy", and "ufz" values with atom
> selections when the newly received timestep is updated, using a trace
> on vmd_frame. I don't have an example script sitting around just
> this moment, however it shouldn't be hard for you to throw one together.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Apr 17, 2007 at 11:44:30PM +0900, preeda wrote:
> > Dear John and other VMD users,
> >
> > Now I perform IMD simulation by running NAMD and VMD in real-time and
> > use a PHANTOM to apply a force on a protein through a tool devices
> > provided in VMD option.
> >
> > Do you know how can I obtain a force data that I applied during the IME
> > simulation and also trajectory data of a PHANTOM?
> > I would like to analysis the force curve and trajectory data of a
> > PHANTOM during the IME simulation.
> >
> > If anyone knows on how to obtain these data, any suggestion will be
> > greatly appreciated.
> >
> > Thanks,
> >
> > Preeda
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078