[gmx-users] Re: REMD analysis

Mark Abraham mark.j.abraham at gmail.com
Fri May 17 16:10:23 CEST 2013

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.


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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