[AMBER] LES, Umbrella sampling and/or NEB

From: Stregone <stregone.protonmail.com>
Date: Thu, 16 Feb 2017 06:50:59 -0500

Dear AMBER users,

There is a protein which has several cavities.
In theory this cavities should close and open (gate). At the beginning,
the cavity is opened, so using long MD, we intent to get the moment
when it close. Unfortunately, until the moment, long simulations does
not show evidence of such event happening. Given cavity has a gate,
by two arms. I am trying to force this gate to close moving those arm
close to each other.

After going through the manual (AMBER 14), I did find that 3 available
MD approaches could be used : LES, NEB and the umbrella sampling.
The question is, are those approaches appropriated for such task
(force to close the gate and look its stability over time)?
Is there maybe other technique/method that could be used for such task ?

I would appreciate any help and/or advise regarding this matter.

Best regards,
AMBER mailing list
Received on Thu Feb 16 2017 - 04:00:03 PST
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