The probability of hydrogen bond formation and hydrogen bond angle

User discussions
1

Hi, I understand the probability of hydrogen bond formation is defined as ([Linse, 1987][Liu et al., 2005]).
060e22243c3e5d3603abd5a6aeffd827
where NHB is the average number of hydrogen bond at a local aqueous phase region, and NC represents the coordinate water molecules number around single water molecules in that region. I want to know how to calculate NHB and NC.

Secondly ,When I did the hydrogen bond angle distribution, I found that there was very little difference between the results. I want to know how to divide the region and then calculate the angular distribution within the region. Thank you.

angle
angle3216×2462 41.9 KB

2

gmx hbond allows using geometric definition of hydrogen bonds to define them throughout the structure.
More information: https://manual.gromacs.org/current/onlinehelp/gmx-hbond.html

3

I’m sorry, I don’t think I understand you. You Didn’t answer my question. I have browsed the pages you provide many times before. But in GMX HBOND I don’t see how to divide the region and calculate the hydrogen bond angle, or how to calculate NHB and NC