Hi David,
If it is a COM distance variable, then you could just use the fxyz variable
as Callum shows in his tutorial (
https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial). If the
reaction coordinate is complex, I think an alternative is the NFE toolkit,
but I have never used this one mysel (
https://ambermd.org/tutorials/advanced/tutorial31/index.html).
Hope it helps,
El sáb., 18 ene. 2020 a las 14:17, David Case (<david.case.rutgers.edu>)
escribió:
> 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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--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Mon Jan 20 2020 - 07:30:01 PST
