VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 29 2003 - 15:11:40 CDT

Dear Jeroen,
  Have you tried a simple test molecule with an appropriate NAMD
configuration file? Try the "brief IMD tutorial" alanin example and
tell me if you have the same trouble with that one:
  http://www.ks.uiuc.edu/Research/vmd/imd/tutorial/

It could be that you'll need to scale down your tracker, and/or significantly
scale down the forces being applied to the simulation in order to work with it
in your CAVE, particularly since you won't get any force feedback when
running in the CAVE. Without force feedback its easy to over-do the
forces you're applying. Let us know if you need more help with this.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 29, 2003 at 04:32:29PM +0200, Jeroen Akershoek wrote:
> I'm messing around with NAMD simulations and displaying them with VMD via the IMD plugin.
> The visualisation works fine. The thing is, I want to interact with my simulation. Tug on a couple of atoms and all.
> So I create a tool (pinch for example) and tug on an atom. The NAMD simulation exits with the following message:
>
> ERROR: Atom 351 velocity is -13622.1 1574.97 -17427.8 (limit is 10000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Exiting prematurely.
>
> No matter how careful I am, I can never move it slow enough to make it work.
>
> I'm running 1.8.1, custom build with CAVE support and we're using the cavetracker to manipulate the atoms
>
> Regards,
> Jeroen
>
> --
> Jeroen Akershoek, VR Specialist
> SARA Computing and Network Services
> tel: +31 20 5923000 fax: +31 20 6683167
>
> A polar bear is a rectangular bear after a coordinate transform. 

-- 
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