Re: [AMBER] aMD tutorial

From: Jason Swails <>
Date: Sun, 14 Jul 2013 23:50:04 -0400

On Wed, Jul 10, 2013 at 5:14 AM, Jerome EBERHARDT <> wrote:

> Dear Amber Developers and Users,
> I ran some aMD simulations on a protein's domain (about 230 residues) and
> now I am looking for a tutorial that explains in details how to reweight a
> trajectory. I saw on this thread
>, there will be such a thing
> but for the moment I didn't find anything.
> Does anyone know how to find this tutorial ?

AFAIK there's a tutorial in the works, but it isn't finished yet. At the
moment I think you're stuck trying to write your own script to reweight
your data from the equations in the original papers out of the McCammon

I think there is some work going into incorporating this stuff into
cpptraj, but I don't know that it made it into the AmberTools 13 release
(relevant information would be in the manual if it did).

It's possible that someone with available scripts may chime in here and
provide them, but alas I am not one of those people.

Good luck,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Sun Jul 14 2013 - 21:00:03 PDT
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