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
--
========================================
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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