I am a student researcher, and am currently using the earlier 1.2.0 version of Avogadro for my academic research. I have been successful in generating an IR spectra for several gaseous molecules that I am hoping to collect data on, such as H2O and CO2; however, would like to get some assistance on how to accurately perform the same procedure with multiple molecules in one file?
For example, I have a file with multiple H2O molecules and have run the auto-optimization with the MMFF94s force field, but generating a spectra of that produces a long list of absorption frequencies (which may be accurate due to the changed molecular dynamics of the file). However, one notable point is that the Avogadro CML file views the separate H2O molecules as one molecule with the chemical formula of “H12O6,” for example.
I would greatly appreciate information regarding how to properly create Avogadro representations of clusters of the same molecule in order to collect accurate data. Thank you for all of the help in advance, and Happy New Year!
P.S. I am utilizing the MOPAC2016 package along with Avogadro to view vibrational spectra.