You can find it in Amber manual.
Original Message
From: Ayesha Kanwal
Sent: Saturday, 14 November 2015 20:34
To: AMBER Mailing List
Reply To: AMBER Mailing List
Subject: Re: [AMBER] how to plot a graph for enthalpy
i also want to know where i can find information about -eo flag for dumping a CSV file. i want to read about it before using it please send me helping link for it.
> From: ayesha_comsian.hotmail.com
> To: amber.ambermd.org
> Date: Sat, 14 Nov 2015 19:43:46 +0500
> Subject: Re: [AMBER] how to plot a graph for enthalpy
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Nov 14 2015 - 08:00:04 PST
