Re: [AMBER] SMD at constant force

From: Jason Swails <>
Date: Mon, 4 Jul 2016 22:34:12 -0400

On Mon, Jul 4, 2016 at 10:06 PM, Ming Tang <> wrote:

> Dear list,
> I want to study the viscoelasticity of my protein using SMD at constant
> force. I want to impose a instantaneously constant force to the protein,
> and monitor the deformation-time relationship. The deformation of the
> protein is not linear with the applied force. After looking at the amber
> mailing list archive, I found that SMD at constant force is not directly
> supported in AMBER11.
> Is SMD at constant force directly available in AMBER16 now? If not, is
> there any equivalent way to do it?

​You can use the flat-well potential to ensure that the entire reaction
coordinate resides in the "linear" portion of the flat-well potential. You
will need to set r1, r2, r3, and r4 such that the reaction coordinate you
are probing is biased by a linear function (whose derivative -- the force
-- is a constant) with the desired slope.

​This will require understanding exactly what the flat-well potential is
and then doing a little math (with basic calculus) to figure out how to get
the desired slope in the linear region.

So the answer is "yes, you can do something equivalent" using the NMR
restraints and a little bit of calculus.


Jason M. Swails
AMBER mailing list
Received on Mon Jul 04 2016 - 20:00:02 PDT
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