I suggest you read some background papers on WHAM (e.g. (1) Kumar, S.;
Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. *Journal of
Computational Chemistry*. *1992*, *13*, 1011-1021.). While WHAM can be used
for
REMD and also for umbrella sampling, it is not 'inherent' to either. It's
simply a method
for reweighting statistics. When you have a clear idea what WHAM is and why
you need it,
your may be able to answer more of your own questions.
--Dan
On Tue, Sep 14, 2010 at 12:11 PM, jani vinod <genomejani.gmail.com> wrote:
> Thanks for reply.
> I have one more doubt is it necessary to carry out umbrella sampling prior
> to WHAM analysis ?
>
> regards
> vinod
>
> On Mon, Sep 13, 2010 at 6:10 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > regarding input to WHAM program, there are many programs that do WHAM
> > analysis, and inputs will depend on which you use. contacting the author
> of
> > the program would probably be best.
> >
> >
> > On Mon, Sep 13, 2010 at 8:37 AM, jani vinod <genomejani.gmail.com>
> wrote:
> >
> > > Dear Sir,
> > > I want to do heat capacity calculation for my protein for which I have
> > > carried out REMD simulation
> > > I read the paper titled "Calculation of Protein Heat Capacity from
> > > Replica-Exchange Molecular Dynamics
> > > Simulations with Different Implicit Solvent Models" .
> > > I have gone through another literature also but didn't got an
> appropriate
> > > solution for wham analysis (especially input to wham program) .
> > >
> > >
> > > Thanks
> > > vinod
> > >
> > > On Mon, Sep 13, 2010 at 5:16 PM, Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > > > please be more specific- WHAM can be many types of calculations.
> > > >
> > > >
> > > > On Mon, Sep 13, 2010 at 7:45 AM, jani vinod <genomejani.gmail.com>
> > > wrote:
> > > >
> > > > > Dear all,
> > > > > what are steps involved in carrying out WHAM analysis after an REMD
> > > > > simulation.
> > > > > Can REMD trajectories directly be used for WHAM analysis
> > > > >
> > > > >
> > > > > Thanks
> > > > > vinod
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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 Mon Sep 13 2010 - 21:30:03 PDT
