On Wed, Dec 9, 2015 at 8:08 AM, Mahendra B Thapa <thapamb.mail.uc.edu>
wrote:
> 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:
https://en.wikipedia.org/wiki/Kullback%E2%80%93Leibler_divergence
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 "
> http://archive.ambermd.org/201508/0109.html" ?
>
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
one.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Dec 09 2015 - 05:30:04 PST
