On Tue, Oct 29, 2013, Vlad Cojocaru wrote:
>
> I did an entropy estimation from a quasi harmonic analysis in ptraj of a
> 150 ns simulation (50.000 frames). I get huge numbers for the
> vibrational entropy (sample output below).
>
> -------------- sample output complex---------------------------
> freq. E Cv S
> cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
> --------------------------------------------------------------------------------
> Total *********** NaN 20143.554
> translational 0.888 2.979 58.245
> rotational 0.888 2.979 62.384
> vibrational *********** NaN 20022.926
That fact that you have all "***" and "NaN" (not a number) in your output
certainly suggests that something is wrong. I don't see how this can easily
be debugged remotely: look for information about the individual frequencies.
Did you superimpose your trajectory (to remove overall rotation and
translation) before running the quasiharmonic analysis? You may want to gain
experience on a simpler, smaller system to make sure you are confident in how
everything is supposed to work.
...dac
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Received on Tue Oct 29 2013 - 05:00:02 PDT
