Re: [AMBER] steered md at constant force

From: Wesley Michael Botello-Smith <>
Date: Thu, 7 Nov 2019 16:15:58 -0800

In answer to (2), you can indeed specify which axis / axes a restraint is
applied along, but only for NMR restraints apparently. (I cant seem to find
a way to do this using the new collective variable options)
I have gotten this to work in AMBER 18 (I don't know if it is possible in
previous versions)

For more details, see page 461 of the AMBER18 manual.

You need to set fxyz=0,0,1. I.e. it will remove force calculation along x
and y axis.
It would also be a good idea to set outxyz=1 as well. That way your NMR
output file will include the x,y, and z components in addition to the total
distance. This is important since you need the z component in particular
without contribution from x and z which are getting ignored.

We are using this currently for pulling a ligand through a transmembrane
channel. It also allows for cylindrical restraints to keep it from
wandering away while being pulled toward the channel mouth.

-Dr. Wesley Botello-Smith

On Thu, Jan 10, 2019 at 1:25 PM Jason Swails <> wrote:

> 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.
> HTH,
> Jason
> --
> Jason M. Swails
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Received on Thu Nov 07 2019 - 16:30:02 PST
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