[gmx-users] interpreting g_hydorder results

[pratibha kapoor]

Please reply and provide some guidance. We have got stuck here.


On Sun, Aug 24, 2014 at 10:56 AM, pratibha kapoor <kapoorpratibha7 at gmail.com
> wrote:

> One of my friends have posted the same query earlier but hasn't got any
> reply. Now, I am also having the same doubt and so posting the question on
> behalf of both of us:
>
> We would like to calculate both distance and angle water orientational
> order. We have made an index file containing all oxygen atoms of water and
> used trjorder as:
> g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1_1 file2_1 -or file1_2
> file2_2
> How to interpret the results of the output files? Both output files
> file1_2 and file2_2 contain the same content. Won't one should contain
> distance and other angle orientational order parameter values?
> Also We expect parameter values to be less than or equal to 1. But the
> values in the file looks something like the following (all greater than 1):
>
>  #Legend   #TBlock   #Xbin Ybin Z t  0   0 0 6.5  0 1 6.5  0 2 4.5  0 3
> 3.5  0 4 6.5  0 5 4.5  0 6 5.5  1 0 6.5  1 1 4.5  1 2 5.5  1 3 3.5  1 4
> 5.5  1 5 4.5  1 6 5.5  2 0 4.5  .
> .
>
>
>           Please help us in interpreting this file.
>
>             Looking forward to reply this time
>
> Any help is highly appreciated.
>