[gmx-users] g_velacc

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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