[gmx-users] Bins in wham analysis

[Justin Lemkul]

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

-- 
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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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