On 2011-05-26 22.48, Nilesh Dhumal wrote:
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
where is the hydrogen?
g_velacc knows nothing about bonds just atoms.
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
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Dept. of Cell & Molec. Biol., Uppsala University.
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