Re: [AMBER] Umbrella Sampling with Z-axis as Reaction Coordinate

From: Jason Swails <>
Date: Mon, 8 Oct 2012 12:38:44 +0200

On Mon, Oct 8, 2012 at 1:57 AM, Dail Chapman <> wrote:

> Dear All,
> I am an undergraduate researcher at Scripps College in California, and am
> trying to partition various small molecules through a lipid bilayer
> membrane in Amber12. It seems most logical to use umbrella sampling with
> the z-axis (i.e., the axis perpendicular to the plane of the membrane)
> distance between the membrane c.o.m. and small molecule c.o.m. as the
> reaction coordinate. Is there a tutorial program available for this, as I
> have not used said technique before? Or would anyone have a suggestion for
> an alternative technique? Any help would be much appreciated. Thank you
> for your time, -Dail

There is no tutorial for this particular type of restraint. However, if
you look at the manual under the nmropt restraint types, there are
plane-point and plane-plane restraint types that may do what you want.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Mon Oct 08 2012 - 04:00:04 PDT
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