[gmx-users] Vibrational spectra of amide I using gromacs

[Mijiddorj B]

Dear Andre

Thank you very much for your quick response.
I am very new for this type of analysis, and I would like to ask further. I
am sorry for that. Is there any good software?
If you have any experience, please suggest me some useful software for the
time series correlation and the Fourier transformation.

Best regards,

Mijiddorj

Should be doable using any standard spreadsheet:
>
> (1) save the bond lengths along the simulation for the bond of interest
>
> (2) compute the time correlation function for these bond lengths (the
> autocorrelation function for this time series)
>
> (3) compute the Fourier transform of the time correlation function
>
> Andre
>
> On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B <b.mijiddorj at gmail.com> wrote:
>
> > Dear gmx users,
> >
> > Hello, I would like to ask vibrational spectra of amide of specific
> > amino acids. Is it possible to analyze from classic MD calculations of
> > gromacs?
> > Or
> >
> > Is there any software that is compatible with gmx trajectories  to
> > calculate the spectra?
> >
> > Best regards,
> >
> > Mijiddorj
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>
> --
> _____________
>
> Prof. Dr. Andr? Farias de Moura
> Department of Chemistry
> Federal University of S?o Carlos
> S?o Carlos - Brazil
> phone: +55-16-3351-8090
>
>
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