[gmx-users] dos command for extracting vibrational spectra for a particular bond

[André Farias de Moura]

Dear Veera,

it can be done by extracting the bond length along the simulation and then
calculating its time correlation function, followed by its Fourier
transform.

Andre

On Tue, Jun 11, 2019 at 7:46 AM veerapandian <veera.pandi33 at gmail.com>
wrote:

> Dear Gromacs users,
>
> I am performing the simulation of ethanol/water mixture and trying to
> extract the vibrational spectra of the O-H stretching band in ethanol.
> In this case, I created the index file for the particular atoms using "a OH
> HO"
> and I used the following command,
>
> gmx dos -f md_1.trr -s md_1.tpr -n index_HOinEtOH.ndx -g dos.log -recip yes
> -vacf dos_vacf.xvg -mvacf dos_mvacf.xvg -dos dos_spectrum.xvg
>
> after that, when I select the group (OH_OH) and I received the following
> error,
>
> "Fatal error: The index group does not consist of whole molecules"
> it seems it does not work for a pair of atoms.
> Is it possible to calculate the vibrational spectra for the particular bond
> in the molecule using gmx dos?
> If yes, could you please tell me what's the problem in the above command.
>
> Your suggestion will be greatly appreciated
>
> Thank you
>
> Best regards,
> Veera
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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