do those codes do T-WHAM?
On Tue, Jul 27, 2010 at 7:15 AM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> Dongshan,
> You can either develop your own code, or use someone else's such as:
> Alan Grossfields: http://membrane.urmc.rochester.edu/content/wham
> or
> John Chodera's: http://www.dillgroup.ucsf.edu/~jchodera/code/WHAM/<http://www.dillgroup.ucsf.edu/%7Ejchodera/code/WHAM/>
>
> Someone else might have a "more straightforward" way of doing this.
> I use my own code, but in its current condition I couldn't lend it out
> *yet*in
> full conscience. :P
> --Dan
>
>
> On Tue, Jul 27, 2010 at 7:43 AM, Dongshan Wei <dswei0523.gmail.com> wrote:
>
> > Hi Everyone,
> >
> > Recently I want to do a ramachandran plot for an Alanine peptide. I
> > did a 10ns temperature REMD simulations with 16 replicas. Now I want
> > to weight the probability for temperatures not at T0 to get the
> > weighted ramachandran plot. I made a quick look through the mailing
> > list and find most WHAM is combined with umbrella sampling. Can
> > somebody give a clear procedure on how to do WHAM based on REMD
> > simulations outputs?
> >
> > Thanks so much!
> >
> > Dongshan
> >
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> >
>
>
>
> --
> Dr. Daniel J. Sindhikara
> Institute for Molecular Science
> E-mail: sindhikara.gmail.com
> Website: http://sites.google.com/site/dansindhikara/
> --
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Received on Tue Jul 27 2010 - 04:30:04 PDT
