[gmx-users] What is the difference between density of states (gmx dos) and vibrational power spectrum (gmx velacc -os)?

[Kneller, Daniel]

Hello Gromacs Gurus,

I'm studying the vibration dynamics of protein.
I'm trying to calculate the density of states (dos) for protein in an MD simulation.
Dos is supposed to be calculated by a Fourier transform of the velocity autocorrelation function.

Both gmx dos and gmx velacc with the -os option appear in the documentation to do this but they give different plots with different axis.

Can someone clarify the difference between these two calculations?

Thank you for your time,

Daniel Kneller
Postdoctoral Research Associate
Neutron Scattering Division
Neutron Sciences Directorate
Oak Ridge National Laboratory