VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 17 2008 - 12:57:37 CDT

Hi,
  If you want to watch the simulation while it's actually running,
you'll need to use the IMD interface, either through the use of the
AutoIMD plugin, or by running the "imd" commands in VMD by hand.
If you run them for yourself, you'll have to have to be sure to
setup the NAMD config file to enable IMD. There's a short tutorial on
this here:
  http://www.ks.uiuc.edu/Research/vmd/imd/tutorial/

The use of IMD will indeed slow down the simulation somewhat as it
requires communication between VMD and NAMD, and this adds a little
more work for NAMD to deal with. That said, there's really no way to
visualize a running MD simulation with no performance cost, so if that's
what you want to do, this is really the only way to do it in practice.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 17, 2008 at 01:42:34PM -0400, Mamta Mohan wrote:
> Dear VMD team,
>
> I would like to know if I can see the structure in water cube going through the motions while simulation is running.
>
> In the last simulation the water cube along with the protein in it, drifted across the screen diagonally from center of the screen to the bottom left corner.
>
> I submitted simulation via vmd command line and did not invoke AutoIMD because I was told it slows down the processing.
>
> I would appreciate your help.
>
> Thank you.
> Mamta Mohan 

-- 
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