> On Nov 14, 2015, at 10:33 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com> wrote:
>
> 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.
Have you checked the manual?
>
>> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 14 2015 - 08:30:03 PST
