From: Marc Baaden (baaden_at_smplinux.de)
Date: Mon Jan 09 2006 - 01:01:03 CST
two things. First, to turn off an applied force on an atom/fragment/molecule
you can use the right mouse button if I remember correctly (that is if you
are applying the force via the mouse). That should turn off the force
instantly ... sometimes it takes a bit of time to "hit" the atom/fragment in
question, but in principle it does work.
(as an aside, I actually think there is a minor bug there somewhere because
the selection of the atom does not always work properly...even if you use a
real simplistic test system like just one toy atom, which you can make
really big to be sure to hit it. This does not only hold for turning off the
force, but also for turning it on after a couple of on/off cycles.
As I think that this is a VMD issue, I also CC the message to the VMD
However the second thing is that you might run into some oldfashioned physics,
something called inertia, which makes your molecule continue to move even
after you turned off the force. So it might actually sometimes be necessary
to use a counter force to stop your molecule.
Hope that helps,
>>> Richard Wood said:
>> I guess that I wasn't clear.
>> I'm using NAMD along with VMD to run an interactive/steered MD calculatio
n, as per "How to run Interactive Molecular Dynamics" at http://www.ks.uiu
c.edu/Research/vmd/imd/tutorial/. Under the Mouse menu of VMD, one can tu
rn on forces to "move" a molecule interactively during a simulation run in
NAMD. However, I would like to turn these forces off at some poijnt, oth
erwise my molecule (a sugar) moves out of the protein that it is bound to,
and I don't want that to happen.
-- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden_at_smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
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