GROMACS version: 2018.4
GROMACS modification: No
I used the velacc module of Gromacs to compute the velocity autocorrelation function. But I’m confused about the output file by velacc.
Here is the order I used: gmx velacc -f water500.trr -s water500.tpr -n index.ndx -b 1 -e 9 -mol yes -normalize no -o vac.xvg
The equation of velocity autocorrelation function is: Cv(τ) = <vi(τ) · vi(0)>
The result of velocity autocorrelation function at the beginning time is 1 shown in vac.xvg file. But Cv(0) = <vi(0) · vi(0)>. and It seems that this value is not 1.
Then, Could anyone please help me to understand this?