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

From: Jason Swails <>
Date: Sat, 14 Nov 2015 06:54:33 -0500

On Sat, Nov 14, 2015 at 5:09 AM, ayesha afzaal <>

> Hi all,
> i want to know if i want to plot graph for enthalpy how is it possible ?
> because in Amber advanced tutorial when i used given mdcrd file it only
> generates one value for Delta G.
> i put the following inputs for
> is
> it possible if i use 1000 frames then also calculate 1000
> binding energies ? how can i plot graph for it please guide me.
> Input file for running PB and GB
> &general
> endframe=50, verbose=1,
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /

​You can use the -eo flag to dump a CSV file that contains *all* of the
energy components for every frame. Then you can graph that information
however you want.

Note that this isn't *really* going to be an enthalpy, as GB and PB both
calculate solvation *free energies* (but for a single snapshot).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sat Nov 14 2015 - 04:00:03 PST
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