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

[yyten]

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

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!

[alevilla]

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

[carbai]

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!