GROMACS version: 2019.6
GROMACS modification: Yes/No
I wish to calculate the tetrahedral order parameter of water surround a protein residue of interest like the figure below:
I saw gmx hydorder is used for this analysis. However, the output of the program is rather confusing, giving something like below:
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.
Can anyone kindly help to explain these outputs? and whether I am doing the correct step in analysis.