VMD-L Mailing List

From: Marc Baaden (baaden_at_smplinux.de)
Date: Fri Jun 13 2003 - 05:35:45 CDT

Dear Jim,

jim_at_ks.uiuc.edu said:
>> In the meantime, the "velocityQuenching on" option can be specified
>> during normal dynamics to give a very crude minimizer that would
>> respond to IMD forces.

thanks for this hint. This is working marvellously.
But now I have a conceptual problem in understanding the different
tools available in VMD to interact with this minimization.

If I simply use the mouse and apply forces to atoms/residues, the
effect is what I would expect. Obviously with the mouse there is
no force feedback, though.

The trouble I have is when I try to use our phantom to interact
with the minimization. The only result that is about what I want
is using the "pinch" type of tool. But it behaves strangely, with
overdimensioned force arrows which are sometimes in directions where
I would not expect them. Any ideas ?

Initially I rather thought using the tug and/or spring tool, but
they seem to have no effect on the minimization ?? (in contrast eg
to the mouse/force approach)
Why is this ?

And is there a similarly simple way to apply the force to the whole
residue instead just one atom (like with the mouse) for the tools ?

Thanks in advance,
  Marc Baaden

NB: this is on a very simple alanine test case, so minimization is
    almost instantaneous and system size should not play a role. 

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden_at_smplinux.de      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217