Hi Saman,
histograming is just another function of cpptrag, check the hist and hist2d commands. Basically, when you have a given criterium for which you want to study the population behavior of your system (say for example, your system may exist in a hydrated or de-hydrated state), you can define a dataset by giving it a name on cpptraj, and then ask the hist command to produce a population graph (histogram) based on that population.
For example, say you have a dataset telling you the number of waters in your pocket for each snapshot, and you have called this dataset "waterinmypocket". Now, by plotting the dataset you might notice that the most waters you have is say 10, the least is 2. Then, you may ask hist to plot a histogram with the following command:
hist waterinmypocket,2,10,1 out waterinmypockethist.gnu
This will produce a histogram based on you dataset waterinmypocket, which will have a range of 2-10, will separate the bins (subsections) in steps of 1 (i.e. 2 waters, 3 waters, ... , 10 waters), and output all of it into a gnuplot readable file called waterinmypockethist.gnu. If your system is trully in two unique states, you should see two humps on your histrogram.
Manuel
-----Original message-----
From:Saman Yousuf ali <
saman.yousufali64.yahoo.com>
To:mmaestre <mmaestre.gate.sinica.edu.tw>,AMBER Mailing List <
amber.ambermd.org>
Date:Thu, 22 Sep 2016 13:00:29
Subject:Re: [AMBER] Plot activesite water vs time.
Dear Manuel,Many thanks for the prompt reply and advice, I willtry to follow your suggestions. I have one more query, kindly elaborate histograming the water populations or share any example/link.
Thanks,Saman
On Thursday, September 22, 2016 9:49 AM, mmaestre <mmaestre.gate.sinica.edu.tw> wrote:
Hi Saman,
Check out the GIST or GRID features in cpptraj (the GIST tutorial on the amber website is really good: http://ambermd.org/tutorials/advanced/tutorial25/). If you're only interested in checking the number of waters, I think just using either the "hbond" command or a combination of "closest" and "distance" in cpptraj, should work. You could use that either for histograming the water populations, or as a dataset to apply via "filter", to obtain the snapshots in your trajectory which are in your favorite hydration state.
I hope this helps,
Manuel
-----Original message-----
From:Saman Yousuf ali <saman.yousufali64.yahoo.com>
To:AMBER Mailing List <amber.ambermd.org>
Date:Thu, 22 Sep 2016 12:24:38
Subject:[AMBER] Plot activesite water vs time.
Dear All,
I have a trajectory file and I would like to plot the number of water molecules within a distance from a ligand in time or study thermodynamicproperties of the water clusters over trajectory. I've been trying to figure out how to do it via cpptraj but I couldn't find anything.
I hope you can help me.
Thanks,Saman
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Received on Wed Sep 21 2016 - 22:30:04 PDT
