This plugin provides a graphical interface to compute spectral densities from trajectories using time series data created with the measure dipole command in VMD and a custom plugin to compute the auto-correlated fourier transform. The spectral density plugin also supports a selection of thermal corrections to the peak intensities. You have to have a trajectory already loaded and have the option to view the resulting spectrum in a MultiPlot window and write it to a file.

Remarks

In order to get meaningful results, the selection of atoms have to have (partial) charges assigned, so loading a corresponding topology file, that contains that information is recommended. For cases, where this is not available, you have the options to either guess charges using the CHARMM guess routine from the APBSrun plugin or to load a atom name to charge mapping from an external file. Instead of using the simple guess, you may want to use the AutoPSF plugin to create a matching .psf file for your system.

This plugin can also be used to compute spectral densities from ab initio MD simulations, if one has computed maximally localized Wannier functions along the trajectory. A corresponding manually loadable charge mapping would look like be following (element X stands for the Wannier centers):

     # pseudopotential valence charges from cpmd run. 
     Zn  12.0 
     O    6.0 
     N    5.0
     C    4.0
     H    1.0
     X   -2.0 # electron pairs from localization

Author

Axel Kohlmeyer.