Dear Dr. David Case:
Thank you for your clarification. After reading several materials, I
figured out that Eq.35 and 36 should be the ones NMA used to convert
vibrational frequencies to internal energy and entropy. Although I am still
struggling in the relationship between MM/PBSA energies and NMA
energies...but I will dig deeper in textbook.
Thanks again for your time!
Best,
Guqin
On Fri, Apr 21, 2017 at 10:34 PM, David Case <david.case.rutgers.edu> wrote:
> On Fri, Apr 21, 2017, Guqin Shi wrote:
> >
> > Thank you for your reply. I agree that Hvib and Svib are not clearly
> > defined here. I learned two terms come from here:
> > http://www.colby.edu/chemistry/PChem/notes/NormalModesText.pdf .
>
> This is generally a good exposition, but I must say that I cannot easily
> follow what is being argued around Fig. 5. It doesn't seem to be making
> conclusions in a context relevant to MM/PBSA calculations. We assume that
> the errors arising from using classical mechanics rather than quantum
> (nuclear) mechanics cancel in the two end states. But those errors are
> sensitive to high-frequency vibrations, not low-frequency ones.
>
> > Are the S and E in nmode() program calculated from the two
> > equations above?
>
> See eqs. 35 and 36 in the pdf file referred to above. Those are what is
> printed by the nmode() routine.
>
> ...dac
>
>
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--
Guqin SHI
PhD Candidate in Medicinal Chemistry and Pharmacognosy
College of Pharmacy
The Ohio State University
Columbus, OH, 43210
https://www.linkedin.com/in/guqin-shi-029bb634
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Received on Fri Apr 21 2017 - 21:30:02 PDT
