Entropy calculation as a function of time

[Mandira Dinda]

Hello,

          Is it possible ti calculate entropy as a function of time?From earlier discussion what I have understood that I have to calculate the entropy  in 0-10, 0-20...0-100 and so on ns time intervals if my trajectory is of total 1500 ns.I have a doubt that after calculating the entropy in that way during plotting I have to plot the cumulative entropy value vs time? I am using the following command to calculate the entropy :

 carma -v -w -fit -force -segid A -atmid ALLID newdcd-1.dcd newpsf.psf

carma -v -cov -eigen -mass -force -temp 300 -last 1000 -atmid ALLID carma.fitted.dcd  carma.selected_atoms.psf > carma_entropy1k.txt

carma -v -w -fit -force -segid A -atmid ALLID newdcd-1.dcd newpsf.psf

carma -v -cov -eigen -mass -force -temp 300 -last 2000 -atmid ALLID carma.fitted.dcd  carma.selected_atoms.psf > carma_entropy1k.txt

and so on

Best Regards,

Mandira Dinda

[Nicholas M. Glykos]

> Is it possible ti calculate entropy as a function of time?From
> earlier discussion what I have understood that I have to calculate the
> entropy in 0-10, 0-20...0-100 and so on ns time intervals if my trajectory
> is of total 1500 ns.I have a doubt that after calculating the entropy in
> that way during plotting I have to plot the cumulative entropy value vs
> time?

This is indeed the approach used in the original papers that carma applies.
See https://doi.org/10.1063/1.1401821 and https://doi.org/10.1016/0009-2614(93)89366-P



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Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, https://utopia.duth.gr/glykos/