Re: [AMBER] on The Nudged Elastic Band Approach (Tutorial 5)

From: Carlos Simmerling <>
Date: Fri, 20 Apr 2012 08:01:17 -0400

I don't think NEB is a good approach for this. In fact, I'm not sure any
calculation can give you this number.
NEB is meant for generating a pathway between 2 defined structures. In
folding, the unfolded state is not a single structure, and the size of that
ensemble (entropy) is a critical part of the thermodynamic stability. For
this any many other reasons, I don't think this is currently tractable.

On Wed, Apr 18, 2012 at 5:42 AM, Acoot Brett <> wrote:

> Dear All,
> Based on your experience, is the The Nudged Elastic Band Approach
> calculation for a 40, 000 Da protein fast or slow? Or it takes long time as
> production MD?
> Do you get the Tm (melting temperature) of your protein based on this
> method?
> I am looking forward to getting a reply from you.
> Cheers,
> Acoot
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Received on Fri Apr 20 2012 - 05:30:03 PDT
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