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

[Mijiddorj B]

 Dear Andre,

Thank you very much for your kind responses.
According to your suggestion, I calculated the bond length as a function of
time. The auto-correlation function was generated by gmx analyze. Then, I
used the xmgrace for the Fourier transform of the Auto-correlation function.
Is the workflow right? The result data does not look like some spectra. How
can I convert it into vibrational spectra and how can I adjust the unit?
If possible, please advise me?
Thank you again for your time.

Best regards,

Mijiddorj


> ------------------------------
>
> Message: 6
> Date: Wed, 8 Jan 2020 22:33:56 -0300
> From: Andr? Farias de Moura <moura at ufscar.br>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Vibrational spectra of amide I using gromacs
> Message-ID:
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> CAKTwKgrecyH10WMA+Sw_86rHyoP9c6k2XsPknvYoEwiUfkyL1g at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> 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. 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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> End of gromacs.org_gmx-users Digest, Vol 189, Issue 19
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