# The question about gmx h2order

**URL:** <https://gromacs.bioexcel.eu/t/the-question-about-gmx-h2order/7456>\
**Category:** User discussions\
**Created:** [October 24, 2023, 12:22am UTC](https://gromacs.bioexcel.eu/t/the-question-about-gmx-h2order/7456 "2023-10-24T00:22:00Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Wade](https://avatars.discourse-cdn.com/v4/letter/w/9de053/32.png) [@Wade](https://gromacs.bioexcel.eu/u/Wade)\
**Post date:** [October 24, 2023, 12:22am UTC](https://gromacs.bioexcel.eu/t/the-question-about-gmx-h2order/7456/1 "2023-10-24T00:22:00Z")

</div>

GROMACS version: 2022.6  
GROMACS modification: No

Dear all users,

I am doing an EOF flow case in a silica nanochannel. (y is height direction and z is length direction)

The water orientation and its angle to y axis is extracted by `gmx h2order` with this commend:  
**gmx h2order -f md.trr -s md.tpr -n index.ndx -o h2order.xvg -b 0 -e 10000 -d Y -sl 600**  
When I check the output xvg file, it is confusing that the output cosine value is different from the one I directly calculate from mu\_x, mu\_y, mu\_z with the simple eqaution:  
**cosθ = (mu\_y/sqrt(mu\_x^2+mu\_y^2+mu\_z^2))**

I try two different water model: SPC/E and TIP4P/2005.  
It seems that the dependency between output cosine value and the calculated value is even larger for TIP4P/2005. (blue is from my calculation, orange is the angle calculated from the cosine value directly from h2order.)  
SPC/E

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/652d2198e522e08a380f893c9df6c46908434486.png)  
TIP4P/2005  
 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/9a3a4b6941fb7621c3157b5849b1568dc69ab772.png)

I am really grateful if anyone know the possible reason for it.  
Thank you for your time and your help.