Re: [AMBER] Questions about Steered MD in Amber

From: Jason Swails <>
Date: Thu, 14 Jan 2016 23:04:56 -0500

On Thu, Jan 14, 2016 at 3:10 PM, Vu Truong <> wrote:

> Hi All,
> I have several questions regarding to the Steered Molecular Dynamics
> simulation in Amber package, which really needs your help.
> 1. Can we apply the external force into a system, for example, a water box
> in the specific direction +z or -z by using Amber?


2. I actually have found that Amber also has the Steered MD method.
> However, I am confused if that external force can be the force applied in a
> specific direction?

​You can "fake" it using dummy atoms tethered to various parts of the
system with restraints and defining your reaction coordinate with the dummy
atom. But in general, I don't think this is possible.

Also, does the parameter *iat *in input mdin file, for
> example I will set 1 and 99, mean that the force will be applied between
> atom 1 and atom 99. Or does it mean among the atom 1 to atom 99?

​A potential energy function will be added for the distance between them
(typically a simple harmonic function). The force obeys Newton's third
law, so it will either pull the two particles together or push them apart,
depending on the assigned equilibrium distance. The force will be applied
to both atoms.

3. As I said, I am trying to apply the external force in a specific
> direction +z /-z for my water box system. So any your advice how I can
> proceed that idea is highly appreciated from me.

​The only program I know about that does this for sure (and for which I
*know* how to do it) is OpenMM. So if I was doing this project, I'd use
OpenMM for it. Amber integrates with the OpenMM project (such that you can
read and write Amber topology, coordinate, and trajectory files) through
the ParmEd module included with AmberTools 16. But you'd need to learn how
to use OpenMM to proceed down this path.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 14 2016 - 20:30:03 PST
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