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<blockquote cite="mid:4D7CC621.9010408@vt.edu" type="cite">
<br>
The reliability of the PMF curve depends on the reliability of
sampling. If you're over-sampling in some regions along the
reaction coordinate and under-sampling in others, then the
weighting is probably wrong and the result inaccurate. I can't
tell exactly from your description what's going on, but if you
have largely overlapping histograms, then your window spacing
and/or force constant settings are inappropriate.
<br>
</blockquote>
I don't really agree with the last point (with the first I fully
agree). In my experience it helps a lot if you have multiple
overlapping histograms. If each histograms overlaps only with the
two neighbors, you typically get large uncertainties - even worse,
since you usually don't know the autocorrelation time, you cannot
even estimate your uncertainty. In addition, I don't see any reason
why WHAM should have problems in case of largely overlapping
histograms.<br>
<br>
My strong suggestion is to use as many histograms as possible, such
that multiple histograms overlap. Make sure (if possible) that each
histogram is independent by starting from independent initial frames
(if these are available). Then you can use the boostrap of complete
histograms (using the so-called Bayesian bootstrap) to compute the
uncertainty:<br>
<br>
g_wham -nBootstrap 100 <b>-bs-method </b>b-hist ...<br>
<br>
As David just pointed out, please have a look into our recent paper:
<a class="moz-txt-link-freetext" href="http://pubs.acs.org/doi/abs/10.1021/ct100494z">http://pubs.acs.org/doi/abs/10.1021/ct100494z</a><br>
<br>
Jochen S. Hub, Bert de Groot and David van der Spoel: g_wham - A
free weighted histogram analysis implementation including robust
error and autocorrelation estimates J. Chem. Theory Comput. 6 pp.
3713-3720 (2010)
<br>
<br>
Cheers,<br>
<br>
Jochen<br>
<br>
-- <br>
<pre class="moz-signature" cols="72">---------------------------------------------------
Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755
<a class="moz-txt-link-freetext" href="http://xray.bmc.uu.se/~jochen/index.html">http://xray.bmc.uu.se/~jochen/index.html</a>
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