Re: [AMBER] Calculate the conduct rate from PMF

From: David A Case <>
Date: Mon, 10 Dec 2018 13:41:29 -0500

On Fri, Dec 07, 2018, Meng Wu wrote:
>I have used the umbrella sampling method with amber16 to get the free
>energy profile of a channel protein, now I want to calculate the conduct
>rate of this channel from the energy barrier, could anybody guide me how
>to calculate it in amber or other related methods? Thank you in advance!

If you want an order-of-magnitude guess, you can apply the Arrhenius

Getting better estimates generally requires a *lot* of work. Amber per
se is not very well equipped in this area, but you should look at the
weighted ensemble method, e.g. in the WESTPA package: this is separate
from, but well-integrated into, Amber.

Others on the list may wish to chime in here.

...good luck...dac

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Received on Mon Dec 10 2018 - 11:00:04 PST
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