[gmx-users] g_velacc

[David van der Spoel]

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
>
>
>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se