On Thu, Jun 5, 2014 at 7:03 AM, James Starlight <jmsstarlight.gmail.com>
wrote:
> 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
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jun 05 2014 - 05:00:03 PDT
