# How to use gmx hydorder to calculate tetrahedral order parameter of water

**URL:** <https://gromacs.bioexcel.eu/t/how-to-use-gmx-hydorder-to-calculate-tetrahedral-order-parameter-of-water/1685>\
**Category:** User discussions\
**Created:** [March 4, 2021, 4:55pm UTC](https://gromacs.bioexcel.eu/t/how-to-use-gmx-hydorder-to-calculate-tetrahedral-order-parameter-of-water/1685 "2021-03-04T16:55:59Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![yyten](https://avatars.discourse-cdn.com/v4/letter/y/839c29/32.png) [@yyten](https://gromacs.bioexcel.eu/u/yyten)\
**Post date:** [March 4, 2021, 4:56pm UTC](https://gromacs.bioexcel.eu/t/how-to-use-gmx-hydorder-to-calculate-tetrahedral-order-parameter-of-water/1685/1 "2021-03-04T16:56:00Z")

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GROMACS version: 2019.6  
GROMACS modification: Yes/No

Dear all,

I wish to calculate the tetrahedral order parameter of water surround a protein residue of interest like the figure below:

[https://www.nature.com/articles/ncomms6773/figures/5](https://www.nature.com/articles/ncomms6773/figures/5)

I saw gmx hydorder is used for this analysis. However, the output of the program is rather confusing, giving something like below:

> [@](#):
>
> #Legend  
> #TBlock  
> #Xbin Ybin Z t  
> 0  
> 0 0 8.50000  
> 0 1 8.50000  
> 0 2 8.50000  
> 0 3 8.50000  
> 0 4 8.50000

A post on researchgate reveals that gromacs is outputting the Z coordinates instead and recommended to add the -debug 1 to the command to force output of the angle and distance which gives the output as follows. However, the output is still rather confusing to me.

> [@](#):
>
> # This file was created Fri Mar 5 00:19:56 2021
> 
> # Created by:
> 
> # :-) GROMACS - gmx hydorder, 2019.6 (-:
> 
> # 
> 
> # Executable: /usr/local/gromacs/bin/gmx
> 
> # Data prefix: /usr/local/gromacs
> 
> # Working dir: /media/yiyang/gromacs/cd44s\_640\_dppc/Hydorder
> 
> # Command line:
> 
> # gmx hydorder -f anneal\_PBC.xtc -n ri\_1.ndx -s anneal.tpr -o file\_1 files\_2 -or file\_1 file\_2 -b 125000 -e 126000 -debug 1
> 
> # gmx hydorder is part of G R O M A C S:
> 
> # 
> 
> # Gravel Rubs Often Many Awfully Cauterized Sores
> 
> # 
> 
> @ title “S\sg\N Angle Order Parameter / Meshpoint”  
> @ xaxis label “(nm)”  
> @ yaxis label “S\sg\N”  
> @TYPE xy  
> 0  
> 0.438926 0.438926 0.625769 0.000000  
> 0.438926 0.438926 1.877306 0.000000  
> 0.438926 0.438926 3.128843 0.000000  
> 0.438926 0.438926 4.380380 0.000000  
> 0.438926 0.438926 5.631917 0.000000  
> 0.438926 0.438926 6.883455 0.000000

Can anyone kindly help to explain these outputs? and whether I am doing the correct step in analysis.

Thank you!

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [March 12, 2021, 11:35am UTC](https://gromacs.bioexcel.eu/t/how-to-use-gmx-hydorder-to-calculate-tetrahedral-order-parameter-of-water/1685/2 "2021-03-12T11:35:17Z")

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Hi,  
Maybe you can contact the authors of the paper to know exactly how they perform the analysis.  
Best regards  
Alessandra

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**Author:** ![carbai](https://avatars.discourse-cdn.com/v4/letter/c/a88e4f/32.png) [@carbai](https://gromacs.bioexcel.eu/u/carbai)\
**Post date:** [October 26, 2021, 7:02pm UTC](https://gromacs.bioexcel.eu/t/how-to-use-gmx-hydorder-to-calculate-tetrahedral-order-parameter-of-water/1685/3 "2021-10-26T19:02:33Z")

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Hi,

Have you done this?  
I am trying to do the same but I can’t understand what is printed in the output file.

Thank you!