Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms?

From: Feng Pan <>
Date: Sun, 19 Jan 2020 11:31:08 -0500


The NFE module can do this, I just gave the example in the tutorial
the customized reaction coordinate is the Z component of distance,

Basically if you want to define the z-component of COM you need some coding
but should not be very hard, I have the instructions
to modify the codes in the tutorial.


On Sat, Jan 18, 2020 at 8:15 AM David Case <> wrote:

> Is there a built-in way in pmemd to define a progress variable (aka
> reaction coordinate) for umbrella sampling to be the z-component of the
> center-of-mass of some group of atoms?
> We have a lipid bilayer with the normal along the z-axis, and would like
> to estimate a PMF for pulling a peptide out of the membrane.
> Suggestions for other/better ways to do this are also welcome.
> ....thx...dac
> _______________________________________________
> AMBER mailing list

Feng Pan
Florida State University
Department of Statistics
AMBER mailing list
Received on Sun Jan 19 2020 - 09:00:01 PST
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