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

From: Stephan Schott <>
Date: Mon, 20 Jan 2020 16:12:55 +0100

Hi David,
If it is a COM distance variable, then you could just use the fxyz variable
as Callum shows in his tutorial ( If the
reaction coordinate is complex, I think an alternative is the NFE toolkit,
but I have never used this one mysel (
Hope it helps,

El sáb., 18 ene. 2020 a las 14:17, David Case (<>)

> 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
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> AMBER mailing list

Stephan Schott Verdugo
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
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Received on Mon Jan 20 2020 - 07:30:01 PST
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