[gmx-users] Re: REMD analysis

[bharat gupta]

Dear Sir,

The the default bin width is 0.1 which I used for plotting the graphs.
Another question is about your last reply to my thread "exchange acceptance
is a poor proxy for sampling efficiency". Sorry to ask this, but how to
check whether the sampling efficiency is optimal or not (what should be
optimal sampling efficiency) ??

On Fri, May 17, 2013 at 11:10 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Histograms 101: The smaller your bin width, the more variations you see.
> The more samples you have, the fewer variations you see. A histogram that
> does not mention either of this is a work of fiction.
>
> The number of degrees of freedom in the potential energy distribution is
> also a factor in whether the distribution will look smooth for a given bin
> width and number of samples.
>
> Mark
>
> On Fri, May 17, 2013 at 3:51 PM, bharat gupta <bharat.85.monu at gmail.com
> >wrote:
>
> > Dear Sir,
> >
> > I tried plotting the PE overlap using the following way :-
> >
> > 1. extract PE of each replica using g_energy
> > 2. get the PE distribution using g_analyze -f potential_0.xvg -dist
> > pot0.xvg
> > 3. used xmgrace to plot all the PE distribution graphs together.
> >
> > The same thing I did for temperature distribution for each replica.
> >
> > Here's the file for both PE overlap (
> > https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png)
> > temp distribution (
> https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png
> > )
> > Is this the correct way ??
> >
> >
> > But the plot doesnot look like this (
> > https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg).
> Do i
> > have to normalize the data and then plot in order to get a smooth plot
> like
> > this one??
> >
> > --------
> > Bharat
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