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

From: Aron Broom <>
Date: Fri, 20 Apr 2012 10:21:32 -0400

Yes, I second Carlos on this.

You could of course try biasing your simulation along a reaction coordinate
like the radius of gyration, maybe using the ncsu codes or simple umbrella
sampling (maybe NEB can do something similar, but I've never used it). But
these approaches can more or less work for maybe a 20 amino acid protein,
like a single beta-hairpin, a single long helix, or maybe if you went
larger it would work for something extremely fast folding (few local minima
in the folding landscape) like the villin headpiece at 70 amino acids. But
for your 350 amino acid protein, there are so many more degrees of
freedom. That's not to say that it wouldn't work, but, you'd have to
simulate for a LONG time, in order to get anything approaching a converged

Maybe with implicit solvent and a lot of simulation time it is possible?
You'd want to have multiple simulations contributing to the same
calculation. Certainly this is a problem that is currently not solved.


On Fri, Apr 20, 2012 at 8:01 AM, Carlos Simmerling <> wrote:

> 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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> > AMBER mailing list
> >
> >
> >
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Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Fri Apr 20 2012 - 07:30:06 PDT
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