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

From: James Starlight <jmsstarlight.gmail.com>
Date: Thu, 5 Jun 2014 13:03:46 +0200

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).


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Received on Thu Jun 05 2014 - 04:30:02 PDT
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