Thank you very much!
On Mon, Feb 25, 2013 at 9:41 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Feb 25, 2013 at 12:33 AM, colvin <colvin4367.gmail.com> wrote:
>
> > Hi all,
> >
> > I calculated the dihedral angles (D1, D2) for a molecule and plotted a D1
> > vs. D2 graph. But i would like to know the conformation population
> > distribution of the molecule.
> >
> > My question is:
> >
> > 1. How can i retrieve the number of conformation or the population
> > information with D1 and D2 using ptraj?
> >
>
> You typically cannot do this without histogramming the data, since you're
> drawing a finite number of samples from a continuous coordinate. So to
> calculate the population of a specific D1/D2 combination, you'll have to
> construct a 2-D histogram of your data (numpy can help with this), and then
> simply look at the resulting number in the histogram whose population you
> want. That will be the number of snapshots with D1 and D2 your desired
> values (plus or minus half the bin width, of course).
>
>
> > 2. How can i then use the data to plot a 3D conformational
> > population distribution plot (see the image)?
> >
>
> Then plot that 2-D histogram using some type of plotting program -- e.g.,
> gnuplot, matplotlib, etc.
>
> As a note, your image has an improperly labeled Z-axis -- the population
> must be integer values since a histogram is simply a count. What you
> actually have plotted is a normalized 2D-histogram which represents a
> 2-dimensional probability distribution function (PDF) since the
> double-integral over both dihedrals is equal to 1. This is often
> unimportant for analysis, since the PDF and the un-normalized histogram are
> related by a (normalization) constant, but when you are looking for the
> "number" of conformations with a given set of dihedrals you need to use the
> un-normalized histogram.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Feb 26 2013 - 18:00:03 PST
