[gmx-users] IR Spectra

[André Farias de Moura]

Hi Alex,

g_velacc does just that, but the results only are meaningful after you
adjust your simulation setting. The most important things you should mind
about IMHO: nstvout option in mdp file should be small enough to allow high
frequency vibrations to be captured and the trajectory should last long
enough to capture low frequency modes.

please mind that saving velocities too often for all atoms in a large
system for a very long simulation will produce really large trr files, you
might have troubles with disk space.

Andre

On Wed, Mar 2, 2016 at 12:49 PM, Alexander Alexander <
alexanderwien2k at gmail.com> wrote:

> Hi Andre,
>
> Thanks for your response.
>
> That is the definition of the spectra in general in each program, but what
> I was wondering is how can I do it specifically in gromacs. If any example
> is available ... .
>
> Cheers,
> Alex
>
> On Wed, Mar 2, 2016 at 4:32 PM, André Farias de Moura <moura at ufscar.br>
> wrote:
>
> > in a nutshell: you need to compute the velocity autocorrelation function
> > and then its Fourier transform.
> >
> > you should mind about proper sampling of velocities and trajectory length
> > among other technical issues, but that's up to you to decide, based on a
> > mixture of trial-and-error and some literature survey to see what other
> > people have done (not something new, it has been done before a lot of
> times
> > already - maybe not with GROMACS, but it has been done anyway)
> >
> > I hope it helps
> >
> > Andre
> >
> > On Wed, Mar 2, 2016 at 12:18 PM, Alexander Alexander <
> > alexanderwien2k at gmail.com> wrote:
> >
> > > Dear Gromacs user,
> > >
> > > I want  to calculate the IR spectra for a bulk crystal, I would be so
> > > appreciated if you let me know how to do so in Gromacs.
> > >
> > > Best regards,
> > > Alex
> > > --
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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
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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