Carlos,
The Chodera code is specifically made for T-WHAM. Alan Grossfield has
implemented
T-WHAM a year or two ago. HOWEVER, I had problems with its numerical
stability for T-WHAM.
I believe this is because it handles the DOS in normal space rather than log
space (last I checked).
--Dan
On Tue, Jul 27, 2010 at 8:18 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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/>
> <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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> > > AMBER.ambermd.org
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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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> >
> _______________________________________________
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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 - 05:00:04 PDT
