[gmx-users] Re: REMD analysis

[Mark Abraham]

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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>