VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 05 2007 - 00:58:14 CST

Peter,

On Tue, Dec 04, 2007 at 09:05:58AM +0100, Peter Schellenberg wrote:
> Hi
>
> I have two questions about applying forces in VMD when a MD simulation
> in VMD is running via IMD.
>
> 1. is there a way to switch off all previously applied forces apart from
> clicking with the right mouse button on the individual points on which
> the forces have been applied? It is often hard to catch the resp.
> points, while the simulation is runing, and sometimes small forces are
> applied accidentially and it is hard to see the force vectors.

I assume you're using the mouse for this and not a haptic device or
other VRPN tracker device? The mouse implementation doesn't presently
provide an equivalent of the 'assigned rep' mode provided by the
Tools menu. The mouse force modes aren't as capable as the 3-D input
device variants are, this is one such case where the mouse limitations
are a bit annoying. Let me know if you are indeed using the mouse,
as we might be able to come up with a short-term mouse or keyboard
callback that would address this problem.

> 2. If I apply a force to an atom using the scripts included in the
> tutorial "stretching deca - alanin" , I obverse the relaxation back to
> an alpha helix upon switching off the force. When I use the same
> procedure (with the same parameters) after applying the force to
> 'residue', I do not observe a refolding. It looks like as if the force
> remained, although the graphical force vectors have vanished upon
> clicking on the residue with the right mouse button. Could there be an
> error in VMD?

Well, there could be issues with the interaction of the script with
the mouse forces, or it could be that the last forces sent are being
cached by NAMD and not zeroed out or something like that. I'll have to
look at this in more detail to give a useful answer.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
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