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 Mon Feb 25 2013 - 06:00:05 PST
