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

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 10 Oct 2013 09:45:17 -0400

On Thu, Oct 10, 2013 at 3:51 AM, Baptiste Legrand <bap.legrand.gmail.com>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.

HTH,
Jason

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