Dear,
how to calculate DOS for bulk water using lammps? Do I intend to calculate the water-nanotube later…
Using only this flag, is it possible to capture the three vibrational modes of water (symmetric stretching, bending and asymmetric stretching ) ? I’m using flexible models for water.
compute VACF water vacf
fix fVACF1 water ave/time 1 1 5 c_VACF[1] file 02_vacf/vacf_X-${CNT}.dat
fix fVACF2 water ave/time 1 1 5 c_VACF[2] file 02_vacf/vacf_Y-${CNT}.dat
fix fVACF3 water ave/time 1 1 5 c_VACF[3] file 02_vacf/vacf_Z-${CNT}.dat
fix fVACF4 water ave/time 1 1 5 c_VACF[4] file 02_vacf/vacf_XYZ-${CNT}.dat
run 7000000
water group would be OHH
Could anyone suggest me an efficient method to capture the vibrational modes of liquid water?
Thank you 
The vibrational DOS corresponding to IR/Raman spectra are usually computed from the fourier transform of dipole autocorrelation functions, but if you are just after the frequencies, you can usually also post process velocities or positions since those changes are all connected (and you are not interested in the phase or intensities, the latter usually also require determining the transition moments, which require quantum calculations, so they are not accessible in classical MD). For more on that, I recommend having a look at MD text books or (review) publications on the subject (you may need to dig somewhat into the past).
LAMMPS doesn’t have an integrated tool for that. But you can use existing analysis tools like VMD or Gromacs for which you would need to convert the LAMMPS data file into a suitable .psf or .top file (so that you have the charges), respectively and store (or convert) your trajectory in a suitable supported format.
Please see, e.g.:
https://www.ks.uiuc.edu/Research/vmd/plugins/irspecgui/
https://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-dos.html
If neither of those are convenient or what you are looking for, you may also want to check out the tools listed here: https://www.lammps.org/prepost.html or look through the “Topic of the Month” discussion.
1 Like
Dear Axel,
thank you for the answer.