GROMACS version: 2019.1
GROMACS modification: No
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What command should I use with gmx hbond in order to get a list (text file) of H-bond donors and acceptors as a function of trajectory time?
Why do I need this? To study specifically which H-bonds are fluctuating more during a trajectory (both number and length of H-bonds)
GROMACS does not have the ability to do this, but I wrote a script that can: https://osf.io/3wunt/
You will need to use the -hbn and -hbm options in gmx hbond to create the H-bonding map and corresponding index files. Then you will need to edit these files as noted in the header of the script (it’s a rather dumb script that I wrote many years ago but have not had the need to improve in any way).