Difference between revisions of "Talk:Weighted Histogram Analysis Method"
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| + | == Confusing terminology and wording == | ||
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I was puzzled by "however, this can be misleading as we are not explicitly stating the density of states as the prefactor, Ω." The prior equations are partitions expressed as integrals over spatial coordinates, so I'm not sure what is misleading about not have an explicit density of states. The density of states would seem more relevant if we were integrating over energy dE. | I was puzzled by "however, this can be misleading as we are not explicitly stating the density of states as the prefactor, Ω." The prior equations are partitions expressed as integrals over spatial coordinates, so I'm not sure what is misleading about not have an explicit density of states. The density of states would seem more relevant if we were integrating over energy dE. | ||
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-- Mike | -- Mike | ||
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| + | Mike, | ||
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| + | You were correct about some of the terms not being defined. Each term should now have a definition either on the page itself, or on the [[Definitions|common terms page]]. Part of the extra terms comes from the original WHAM paper by Kumar et al. {{cite|Kumar1992}} where they defined a set of simulated states separately from the set of analyzed states; this gives rise to the double subscript. | ||
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| + | WHAM was developed to work for any restraining potentials along some arbitrary coordinate <math>\xi</math>, so there has been some translations done here to match the original terminology to alchemical terminology. | ||
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| + | I hope the changes to the page make things more clear and feel free to ask any other questions you might have. | ||
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| + | -[[User:Lnaden|Levi Naden]] ([[User talk:Lnaden|talk]]) 11:35, 17 July 2013 (CDT) | ||
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| + | =References= | ||
| + | <references> | ||
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| + | {{cite|Kumar1992|Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A., and Rosenberg, J. M. (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. ''J. Comput. Chem.'' 13, 1011–1021.|http://www.citeulike.org/user/dgront/article/774373}} | ||
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| + | </references> | ||
Latest revision as of 10:35, 17 July 2013
Confusing terminology and wording
I was puzzled by "however, this can be misleading as we are not explicitly stating the density of states as the prefactor, Ω." The prior equations are partitions expressed as integrals over spatial coordinates, so I'm not sure what is misleading about not have an explicit density of states. The density of states would seem more relevant if we were integrating over energy dE.
Subseequently, it seems as though there are a number of symbols which need to be defined; e.g. B_i, lambda_j,i, q_j. Sorry if the definitions are there and I'm missing them!
-- Mike
Mike,
You were correct about some of the terms not being defined. Each term should now have a definition either on the page itself, or on the common terms page. Part of the extra terms comes from the original WHAM paper by Kumar et al. [1] where they defined a set of simulated states separately from the set of analyzed states; this gives rise to the double subscript.
WHAM was developed to work for any restraining potentials along some arbitrary coordinate [math]\displaystyle{ \xi }[/math], so there has been some translations done here to match the original terminology to alchemical terminology.
I hope the changes to the page make things more clear and feel free to ask any other questions you might have.
-Levi Naden (talk) 11:35, 17 July 2013 (CDT)
References
- ↑ Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A., and Rosenberg, J. M. (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comput. Chem. 13, 1011–1021. - Find at Cite-U-Like