[gmx-users] g_velacc

Justin A. Lemkul jalemkul at vt.edu
Fri May 27 14:28:22 CEST 2011

Nilesh Dhumal wrote:
> I am  calculating OH stretching frequency by fourier transform of velocity
> autocorrelation function.
> I could calculate the OH stretching frequnecy by calculating fourier
> transform of OH bond.
> I want to know how gromacs calculate the velocity autocorrelation function
> of a bond (If I define a bond in index file).
> Does is subtract the velocity of hydrogen from oxygen and then
> calculate the autocorrelation function?

See manual sections 8.5.3 and 8.5.4.  I doubt g_velacc does anything this 
complex.  Check the code to be sure, but based on the equation in 8.5.4, it 
would seem not.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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