Re: [AMBER] On the choosing of coordinate for the umbrella sampling

From: Jason Swails <>
Date: Thu, 5 Jun 2014 07:45:56 -0400

On Thu, Jun 5, 2014 at 7:03 AM, James Starlight <>

> Dear Amber users!
> I'd like to compute of PMF along some coordinate specified transition of my
> protein from the inactive R to the active R* form. I'll be thankful for
> someone who could provide me with some tutorial with the guide for
> calculations of the lowest minimum transition pathway between R and R*
> provided in two pdbs and using it for the further PMF as some collective
> variable (e.g combination of eigenvectors or something like this).

​This sounds like another question that is best answered by literature
searches and experimentation.

The art of PMF calculations lies in picking the reaction coordinate (RC)
about which the PMF is computed, and there is no tried-and-true recipe
(that I'm aware of) for picking the ​RC for umbrella sampling. You
typically need some kind of prior knowledge about how the system behaves in
order to pick a PMF. And even then, PMFs are far from unique and different
choices accomplish different goals (compare a 2-D PMF of 2 distances with a
1-D PMF made up of a linear combination of those same 2 distances).

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jun 05 2014 - 05:00:03 PDT
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