Hi,
The resulting ensemble from an aMD simulation is biased. You'll need to
unbias it in order to perform any analysis for which you want an unbiased
answer. This will most likely be ALL analysis, unless you specifically want
to understand something about what the bias itself is doing to the protein
conformations.
You can read this paper to get an idea of how well different reweighting
schemes work for different size systems:
Miao et al. JCTC 2014 -
http://pubs.acs.org/doi/pdf/10.1021/ct500090q
But for large systems it still seems difficult to reweight, and because of
this aMD may not be the right choice for large proteins.
-Christina
On Tue, Aug 9, 2016 at 9:08 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
> I have done aMD so I see that I need to reweigh it before gong for post
> simulation analysis.
>
> So want to know for which kind of analysis I need to do reweighing.
>
> ________________________________
> From: Adrian Roitberg <roitberg.ufl.edu>
> Sent: Tuesday, August 9, 2016 4:04:05 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] for what kind of post simulation analysis I need to
> do reweighing?
>
> reweighing of what ?
>
> Adrian
>
>
> On 8/9/16 11:01 AM, Thakur, Abhishek wrote:
> > Hi
> >
> > I need help to know that for what kind of post simulation analysis I
> need to do reweighing?
> >
> > Is it done for the analysis which include collective variables like PCA
> only? Or I need to do it for distance, angle, RMSD, RMSF, H bonding etc
> also?
> >
> >
> >
> > Thanking you,
> >
> > Abhishek
> > _______________________________________________
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> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
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--
---------------------------------------------------------------------------------------
Christina Bergonzo
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
http://home.chpc.utah.edu/~cheatham/
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Received on Tue Aug 09 2016 - 09:30:02 PDT
