Re: [AMBER] FW: FW: How to use "divergence" command

From: Jason Swails <>
Date: Wed, 9 Dec 2015 08:28:22 -0500

On Wed, Dec 9, 2015 at 8:08 AM, Mahendra B Thapa <>

> Dear Amber users,
> Which formula was used to calculate "divergence" ?

​This is the Kullback-Leibler divergence. The first formula listed in the
Wikipedia article defines this metric: ​

 How this command differs from 'kldiv' command as given in Amber manual 14
> (section 28.12.10) and also as used in the previous post "
>" ?

​kldiv is not a command. It is an option for the kde command, and it
allows you to calculate the K-L divergence for a *continuous* distribution
function constructed from Gaussian kernels centered at each datapoint.
Note that in this case, the *second* formula in the Wikipedia article
applies, as this is now a continuous distribution rather than a discrete


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Dec 09 2015 - 05:30:04 PST
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