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

[André Farias de Moura]

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