Re: [AMBER] Plotting heat maps in AMBER aMD simualtions

From: Brian Radak <>
Date: Wed, 11 Dec 2013 11:10:32 -0500

Presumably this is just basic stat mech, covered in standard texts like
Allen and Tildesley. There was also a paper on analysis of aMD and aMD
replica exchange a few years back that probably has explicit formulas (or
so I would hope):

Fajer, *et al. J. Comput. Chem*. *2009*, *30*, 1719.

They ultimately recommended using MBAR, for example with the pymbar python


On Wed, Dec 11, 2013 at 10:56 AM, filip fratev <>wrote:

> Hi all,
> Recently I asked about the progress of the aMD tutorial and the python
> script to reweight and plot the energies. Is there any progress?
> I think that there are still some open questions, which not received clear
> answer for me:
> May ask for some very simple guide about reweighting procedure? I'd like
> one of my students to make some python script but want to be sure that use
> the correct formula and approach.
> Thanks in advance!
> Regards,
> Filip
> _______________________________________________
> AMBER mailing list

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 Brian Radak                                             :     BioMaPS
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Received on Wed Dec 11 2013 - 08:30:03 PST
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