[gmx-users] Bins in wham analysis

[lloyd riggs]

True, I found the lower bin numbers makes the error change (increase), especially at ends of the run, howevere the mean values were the same.  I also checked with g_sham as comparision, and found again the means the same but differences in error (max and min values if I include all data).  So all three checks gave same mean, different (wider or lower) error (and I guess subsequent varience so is expected).

Interesting note, if I use sham, or wham, running wham on only a single trajectory, then merge them all by hand in a spread sheet (wham output), the wham has the same values as the sham?  Does anyone know why?

Stephan Watkins


-------- Original-Nachricht --------
> Datum: Thu, 26 Jul 2012 06:46:04 -0400
> Von: Justin Lemkul <jalemkul at vt.edu>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] Bins in wham analysis

> 
> 
> 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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