[gmx-users] Re: g_velacc

[Vitaly Chaban]

>
> 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?



The program acts as if your hydrogen and oxygen are identical atoms.


-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216