VMD-L Mailing List

From: Peter Schellenberg (peter.schellenberg_at_ipht-jena.de)
Date: Tue Dec 04 2007 - 02:05:58 CST

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.

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?

Many thanks in advance Peter