Re: [AMBER] restraints in simulations

From: Jason Swails <>
Date: Tue, 26 Jan 2016 10:49:26 -0500


On Tue, Jan 26, 2016 at 10:27 AM, Lara rajam <> wrote:

> Dear Amber !
> Thank you for the reply. I am not interested in steered dynamics , rather I
> want to do a kind of targeted dynamics ,
> So that I can bring the ligand to the receptor binding site from a far
> distance. I have gone through the literatures ,
> but I have problem in handling forces to make the decrease in distance as
> linear component of time,

​You say you don't want to do steered molecular dynamics, but what you
describe wanting to do IS steered molecular dynamics.

What you describe is a non-equilibrium, biased simulation. Steered MD is
implemented by moving the center of a harmonic restraint potential along a
reaction coordinate linearly as the simulation progresses.
​ How is this not what you want to do?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 26 2016 - 08:00:07 PST
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