Re: [AMBER] steered md at constant force

From: Jason Swails <>
Date: Thu, 10 Jan 2019 16:23:13 -0500

On Wed, Jan 9, 2019 at 6:01 AM Batuhan Kav <> wrote:

> Dear All,
> Our system is composed of a lipid bilayer with a single anchored
> glycolipid. We would like to apply a constant force to the center of
> mass of the glycolipid along with the membrane normal (which will be
> z-axis) to study the displacement of certain atoms in the glycolipid as
> a response to this constant force. From an earlier question at the mail
> list (, I see that a
> constant force SMD can be achieved with defining the distance restraints
> (in Amber10), however it seems like the distance restraints are applied
> to certain singular atoms. In this regard, I have three questions:
> 1) Can I apply restraints on center of mass of a certain group of atoms?

You can do this with NMR restraints described in chapter 25.1. It's also
possible to do with the other form of restraints introduced in chapter 21.6
of the Amber 18 manual (these restraints are a little more flexible, but
I'm not sure everything that's available within pmemd.cuda compared to
sander or CPU pmemd).

2) How can I set the applied force to act along only one axis (z-axis)?

I'm not sure if this can be done.

> 3) Is there a way to specify/set the magnitude of the force to a
> constant value?

Indirectly. The potential energy function of the restraint is a flat-well
potential, described in the Amber manual. To get constant force, you need
to make sure that the restraint is in the *linear* part of the potential.
You need to tune the end-points such that the slope of the flat-well
potential at the boundary between the quadratic and linear portions is set
to value of the force you want to pull with. You also have to make sure
you're only pulling over a region of the coordinate that is firmly within
the linear segment.


Jason M. Swails
AMBER mailing list
Received on Thu Jan 10 2019 - 13:30:03 PST
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