[gmx-users] g_velacc

[Nilesh Dhumal]

Hello,

I have calculated the velocity autocorrelation function of OH bond
in glucose molecule. For this calculation I modified the index file. The
modified part is pasted below.

[ O10 ]
  10   20

10 is oxygen no. and 20 is oxygen.

I used following command to calculate the velocity autocorrelation function.

 g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o


My question is how does the prog. calculate the velocity autocorrlation
function.

Does is subtract the velocity of hydrogen from oxygen and then calculate
the autocorrelation function?

I am using gromacs version 4.0.7.

Thanks

Nilesh