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

[David van der Spoel]

Den 2020-02-05 kl. 19:49, skrev 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.

Both tools need long simulations where velocities are saved often, say 
every few fs. Then they need converged simulations, which is not going 
to happen with a protein. These tools are more geared for simulations of 
liquids.
> 
> 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
> 
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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