VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat May 09 2020 - 18:12:29 CDT

Hi Varun, this is really specific to what degrees of freedom you want to
get the entropy of.

A typical approach is to compute the histogram of the degrees of freedom
you are interested in, normalize it so that it represents an estimated
probability distribution, and then use the Shannon formula on it:
https://en.wikipedia.org/wiki/Entropy_(information_theory)

Giacomo

On Sat, May 9, 2020 at 2:02 PM varun dewaker <
varun_dewaker1986_at_remove_yahoo.com> wrote:

> Dear VMD users
>
> I have a question regarding entropy calculation. Is it possible to
> compute the entropy in VMD?
> Or there is any plugin which can calculate this. I have the trajectories
> in dcd format.
> Your response will be valuable for us.
> Thanks
>
>
> *Regards,*
> *Varun Kumar Dewaker*
> *Research Fellow*
> QSAR & Molecular Modelling Lab
> MPC Division (CSN-202)
> CSIR- Central Drug Research Institute
> Lucknow - 226031 (U.P), India
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin