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:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029230/
> Date: Sat, 14 Nov 2015 06:54:33 -0500
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] how to plot a graph for enthalpy
>
> On Sat, Nov 14, 2015 at 5:09 AM, ayesha afzaal <khwahish_2008.hotmail.com>
> wrote:
>
> > 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 mmbsa.in
> > is
> > it possible if i use 1000 frames then MMPBSA.py 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).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat Nov 14 2015 - 07:00:03 PST
