From: Gungor Ozer (gungor.ozer_at_gmail.com)
Date: Fri Apr 25 2008 - 16:17:13 CDT
The answer to your question is TCL forces, where you can apply varying
forces that you could update at each step.
That tutorial might be useful for a start. Please note that this is a
constant velocity pulling at z-direction only. You might wanna modify your
force vector as you wish (using coordinates of the two particular atoms you
Hope that'll help...
On Fri, Apr 25, 2008 at 4:23 PM, Yang Gao <yanggao_at_iastate.edu> wrote:
> Dear all,
> I want to apply an restaint force between two atoms during NAMD run, just
> adding a external force in the line that connect the two atoms, but change
> nothing else. I have searched tutotials but just find in SMD how to define
> constant velocity or force pulling in a fixed direction. But as the atoms
> change their direction during runtime, this may not suitable for my case. I
> hope some of you may know the codes for define the specific interation or
> modify the SMD code to change the direction of the force during runtime.
> Thank you very much.
> Gao, Yang
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