Re: [AMBER] how to plot a graph for enthalpy

From: <>
Date: Sat, 14 Nov 2015 14:55:27 -0600

Hi Ayesha,

   I just share my python codes to plot graph for "enthalpy" in the
tutorial here <>.
  Feel free to modify it. Please let me know if you cannot open the link.


On Sat, Nov 14, 2015 at 11:29 AM, Jason Swails <>

> On Sat, Nov 14, 2015 at 9:43 AM, Ayesha Kanwal <
> >
> wrote:
> > Dear Jason M. Swails,
> >
> > I am giving here a paper link because it cannot attached with this mail
> > for bigger in size, in which author plotted graph for Enthalpy's
> > and Entropy's fluctuations and the accumulated mean values. I exactly
> > want to plot graph like that please take a look on this paper. i could
> > not under stand how can he plot it. and what i
> > have to need for plotting it. here is the link of that paper:
> >
> >
> ‚ÄčIt seems that what that paper calls enthalpy is really just the sum of the
> MM energy terms *including* delta G solvation. This is everything except
> for the normal mode contribution. They presumably wrote a script that
> calculated these composite terms for each frame from the components that
> the MM/PBSA script produces. Their script probably also calculated the
> cumulative average and wrote a file that could be plotted easily.
> Note however, as I mentioned before, that what they are calling the
> enthalpy is not really an enthalpy. It has solvent entropy included.
> So you would need to write a script to take the output of the -eo flag in
> and process it to get the data that they plotted. Or open it in
> a spreadsheet like Excel and do your plot there. There is no tool to
> automatically create these figures for you.
> Alternatively, if you are comfortable with Python, you can extract the data
> directly in a Python script using the API (which is also
> described in the manual).
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Pin-Chih Su (Henry Su)
Center for Pharmaceutical Biotechnology (MC 870)
College of Pharmacy, University of Illinois at Chicago
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Received on Sat Nov 14 2015 - 13:00:03 PST
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