On 7/26/12 3:55 AM, neeru sharma wrote:
Dear Gromacs users,
I have a query regarding the number of bins used in wham analysis.
If I have performed by simulations over 15 umbrellas (15 different
staring structures), what should be the ideal number of bins to
perform wham analysis? Does it depend on the number of umbrellas. For
example:
1) Should I use more than 15 bins in my case, and the one that gives
proper overlap in histogram ?
2) Or any number of bins (even if it is less than 12) can be used, if
I get proper overlap in my histogram output?
Any suggestion is appreciated.
The -bins option has to do with the final PMF profile. The default value is
200, and I would think that setting a low number like 12 or 15 would result in
very poor output. I believe there is some discussion on this in the g_wham paper.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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