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
library:
https://simtk.org/home/pymbar
Regards,
Brian
On Wed, Dec 11, 2013 at 10:56 AM, filip fratev <filipfratev.yahoo.com>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:
> http://archive.ambermd.org/201304/0277.html
> http://archive.ambermd.org/201304/0307.html
>
> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Wed Dec 11 2013 - 08:30:03 PST
