Re: [AMBER] PCA_representation_in_Cpptraj

From: Juan Eiros Zamora <>
Date: Wed, 11 Mar 2015 12:52:48 +0000


Thanks for your corrections on my script. I have one additional
question, when you say
> Jason explained all of this quite well. I will only add that as an
> alternative to 'hist' in one dimension, you can create 1D histograms
> in cpptraj with a Gaussian kernel density estimator using the 'kde'
> command.
> Hope this helps,
> -Dan
Is there any way I can use the KDE to calculate the Free Energy in the
PCA 2D plot? Looking in the Amber manual I've found that the only option
for the hist command is with bins. Or a way where I could do the 1D
histogram with kde command and then transfer it to the PCA projection
file? I think it would be a better idea than selecting myself the bin
size, as Jason mentioned that it is a better solution for this problem.

Thank you for your time,


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Received on Wed Mar 11 2015 - 06:00:04 PDT
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