[gmx-users] Unit of the spectral density

istvan at kolossvary.hu istvan at kolossvary.hu
Mon Jan 5 19:47:00 CET 2004


I am generating spectral density data with xmgrace. I am taking the velocity 
autocorrelation function (g_velacc) and calculate the Fourier transform 
(spectral density) with xmgrace. Spectral density is usually plotted as a 
function of wave number in units of [1/cm]. In Gromacs MD units, spectral 
density is plotted (as "period" in xmgrace) as a function of 1/ps. Dividing 
it by the speed of light (300,000 nm/ps) and multiplying it by 1e07 (cm/nm) 
should give the right units for the abscissa. However, the numerical values 
are off by somethig like a factor of ~10. I was wondering if there is a 
"2Pi" or something like that missing. Has anyone calculated spectral density 
with Gromacs? 

Many thanks, 

  Istvan Kolossvary 

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