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

[André Farias de Moura]

Dear Mijiddorj,

It is a matter of taste, but I like to use xmgrace for that kind of
analysis.

The GROMACS tool gmx analyze can do that for you:
http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-analyze.html

Andre

On Wed, Jan 8, 2020 at 9:18 PM Mijiddorj B <b.mijiddorj at gmail.com> wrote:

> 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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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090