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

veerapandian veera.pandi33 at gmail.com
Tue Jun 11 12:46:55 CEST 2019

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
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

"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,

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