[gmx-users] Re: g_velacc
vvchaban at gmail.com
Fri May 27 09:52:31 CEST 2011
> 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
> 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
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