I agree with Brian. These papers are useful for users of WHAM. I have
written a numerically stable, generally applicable program to perform WHAM
just recently published (the software includes examples of applying WHAM
to REMD in AMBER):
*D.J. Sindhikara.* *Computer Physics Communications*, 182 (2011) 2227–2231
http://dx.doi.org/10.1016/j.cpc.2011.05.008
It would be wise to read the seminal papers on WHAM before applying anyone's
program however (e.g.):
A.M. Ferrenberg, R.H. Swendsen, Phys. Rev. Lett. 63 (1989) 1195.
Specifically, related to your question: what do you mean "include the
temperature factor"? If you mean find the distribution/PMF at an arbitrary
temperature, you would do this by applying WHAM to your energy time series',
extract the energetic density of states, multiply by the "temperature
factor" (Boltzmann weight at target temperature), then use a time series
with the property of interest mapped to the energy to get the appropriate
distributions.
-Dan
On Wed, Sep 7, 2011 at 12:49 AM, Brian Radak <radak004.umn.edu> wrote:
> I am not an expert in temperature replica exchange, but I do make heavy use
> of WHAM and its close cousin MBAR. The papers that come to my mind are
> (there are perhaps others):
>
> Gallichio, et al J Phys Chem B 2005, 109, 6722. - T-WHAM
>
> Chodera, et al J Chem Theory Comput 2007, 3, 26. - PT-WHAM
>
> Shirts and Chodera J Chem Phys 2008, 129, 124105 - MBAR
>
> Happy reading,
> Brian
>
> On Tue, Sep 6, 2011 at 10:20 AM, Catein Catherine <askamber23.hotmail.com
> >wrote:
>
> >
> > Dear Sir/Madam,
> > Any tutorial to teach us how to get PMF energy profile from Replica
> > Exchange Simulations? I learn from previous message in this forum that I
> > can use WHAM, how to incorporate the temperature factor in the analysis?
> > I studied tutorial a7, but it did not include the energy analysis part.
> > Any reference should I read?
> > Best regards,
> > Catherine
> > _______________________________________________
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> > 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 : Wright-Rieman Hall 101
> Graduate Program in Chemical Physics : 610 Taylor 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
> address.
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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 Sep 06 2011 - 16:00:03 PDT
