Re: [AMBER] kinetic

From: Jason Swails <>
Date: Wed, 2 Dec 2015 08:34:35 -0500

On Wed, Dec 2, 2015 at 7:14 AM, Ziba Bahadori <>

> ​​
> Hi every oneI have a questionCan I use amber for kinetics studies?how?

This question is so vague as to have no good answer. There are many
kinetic studies you can do with packages like Amber, and many that you
cannot. Since the answer for the first question is both "yes" and "no",
the answer for the second is undefined. It depends on many factors (what
you're trying to learn, what approximations you are prepared to deal with,
the computational resources you can devote to it, what you *know* about the
process, etc.). Kinetics is a very broad area -- you have diffusive
processes (where diffusion is rate-limiting), chemical reactions with bonds
breaking/forming, binding events, folding/unfolding, ... etc.

This question suggests that your next step should be a literature review,
paying particular attention to articles that study similar things to what
you are trying to do.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Dec 02 2015 - 06:00:06 PST
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