From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Sun Jan 08 2006 - 17:03:28 CST
I guess that I wasn't clear.
I'm using NAMD along with VMD to run an interactive/steered MD calculation, as per "How to run Interactive Molecular Dynamics" at http://www.ks.uiuc.edu/Research/vmd/imd/tutorial/. Under the Mouse menu of VMD, one can turn 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, otherwise my molecule (a sugar) moves out of the protein that it is bound to, and I don't want that to happen.
I hope this clarifies things.
Richard L. Wood, Ph. D. Computational Chemist Cockeysville, MD 21030 rwoodphd_at_yahoo.com
----- Original Message ----
From: Lewyn Li <ll2150_at_columbia.edu>
To: Richard Wood <rwoodphd_at_yahoo.com>
Sent: Sunday, January 08, 2006 13:58:24
Subject: Re: namd-l: Turning off forces in VMD
VMD is a visualization software and doesn't do molecular dynamics on
its own. So, as far as I know, it is impossible to turn off forces
It is possible to turn on an applied force during a MD simulation,
and then turn it off at some later step. I do it with a tcl script,
which I can send to you if you wish. However, switching off a force
does not guarantee that atoms will stop moving.
Hope this helps!
On Jan 8, 2006, at 1:15 PM, Richard Wood wrote:
> Hi all,
> I'm using NAMD/VMD to do some steered MD calculations. I can turn
> on forces to "drag" a molecule in a simulation, but I can't get the
> molecule to stop moving after it's had a force applied to it. How
> does on turn off forces in VMD?
> I also have asked a question about using IMD under Windows, but no
> one responded to that. I'd appreciate a response to both questions.
> Richard L. Wood, Ph. D.
> Computational Chemist
> Cockeysville, MD 21030
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