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

From: Baptiste Legrand <>
Date: Thu, 10 Oct 2013 23:50:31 +0200

Le 10/10/2013 15:45, Jason Swails a écrit :
> 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): 2186–2195)? 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
Thanks for your answer Jason, first I will try with grace.

Best regards,

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Received on Thu Oct 10 2013 - 15:00:05 PDT
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