[gmx-users] Documentation of gmx velacc spectrum and gmx dos

[David van der Spoel]

On 27/07/16 14:55, Hartling, Kathryn wrote:
> UNRESTRICTED / ILLIMITÉE
>
> Dear GROMACS users,
>
> I am new to GROMACS, and I was wondering whether someone could direct me to documentation on exactly what is calculated in the spectrum option (-os) of gmx velacc, as well as the gmx dos function? They don't seem to be documented in the reference manual, and I'm not sure how to deal with the use of arbitrary units.
>
> Thanks,
>
> Katy
>
I created a reminder for gmx velacc
https://redmine.gromacs.org/issues/2019
The spectrum is the square of the fourier transform of the velocity 
autocorrelation function. We encourage users to read the source code :)

gmx dos will be updated in the near future and documented there. The 
present version only computes the quantum correction to the heat capacity.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se