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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>
--
================================ 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
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Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Tue Sep 06 2011 - 09:00:04 PDT
