[gmx-users] Re: REMD analysis

[Mark Abraham]

On Fri, May 17, 2013 at 4:26 PM, bharat gupta <bharat.85.monu at gmail.com>wrote:

> Dear Sir,
>
> The the default bin width is 0.1 which I used for plotting the graphs.
>

That's nice. You need to decide what you need to do about it if you want
graphs that look like those you see reported :-)


> 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) ??
>

Ah, now here's the real question :-) Spacing the replicas for optimal
*flow* is a difficult problem, even for toy peptides, see e.g. papers by
Nadler and Hansmann. Merely accepting exchanges does not imply flow. The
belief is that getting flow enhances sampling, but the latter is hard to
demonstrate without showing that "simulation time to converged sampling"
actually reduces. I'm not aware of anybody who's actually done that - but
it would certainly be an advantage if your application is interested in
data at a range of temperatures.

Mark

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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