Re: [AMBER] Distributions of the phi and psi torsion angles during MD simulations

From: Jason Swails <>
Date: Thu, 10 Oct 2013 09:45:17 -0400

On Thu, Oct 10, 2013 at 3:51 AM, Baptiste Legrand <>wrote:

> Dear all,
> Is there an easy way to make plots to show the distribution of dihedral
> angle values of a molecule during a simulation (probability versus angle
> value, e. g. fig 4 in Protein Sci. 2010, 19(11): 21862195)? For the
> moment, I monitored the torsion angle values during the simulation and I
> calculated an average values (and sdev).

You can either create a normalized histogram or use a kernel density
estimator to construct the probability distribution. There are numerous
programs that will do this for you, including grace, cpptraj, and
numpy/matplotlib (and I'm sure others, like Mathematica, Matlab, and R).
 I'm not sure that cpptraj has a KDE in the released version, but it's
planned for release in AmberTools 14.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Oct 10 2013 - 07:00:04 PDT
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