Dear lammps-community,

I’m accustomed with lammps for a long time but a beginner for computing spectral density. Suppose, I have a molecule X-O-Y, and i want to calculate OX and OY vibrational spectrum by doing fft of vacf. As far as my understanding, I can calculate vacf for a single atom (defined as a group) like, X, Y or O. Then, if i do fft of that vacf(X) then should it refer to OX vibrational spectra ? if not how can it be possible to compute OX vibrational spectra ?

Please help me out. Thanks.

Liu

My two cents.

How about calculating spectra for X, Y and O and then comparing them. The common peaks in X and O should correspond to OX vibrational characteristics and Y and O should correspond to OY.

Dear lammps-community,

I’m accustomed with lammps for a long time but a beginner for computing spectral density. Suppose, I have a molecule X-O-Y, and i want to calculate OX and OY vibrational spectrum by doing fft of vacf. As far as my understanding, I can calculate vacf for a single atom (defined as a group) like, X, Y or O. Then, if i do fft of that vacf(X) then should it refer to OX vibrational spectra ? if not how can it be possible to compute OX vibrational spectra ?

If you use a force field that assigns partial charges to atoms (e.g. Charmm amber, opls, etc.) then you can directly use the spectral density calculator in VMD. It only needs a regular trajectory with position data and the partial charge information, e.g. from the data file.

Axel