Hydrogen bond autocorrelation

User discussions
1

GROMACS version: 2021.4 / 2024
GROMACS modification: No

Hello everyone!

I have two versions of GROMACS: 2021.4 and 2024. For the 2021.4, I manage to compute the hydrogen bond autocorrelation function doing something like: gmx hbond -f md.trr -s md.tpr -ac ac.xvg. It computes the autocorrelation function and the kinetic constants according to Luzar and Chandler, which is what I need. However, when I try to compute it with the 2024 version, I get:

Error in user input:
Invalid command-line options
Unknown command-line option -ac

Is there a way to compute the HB autocorrelation function with this version (2024)? I run most of my calculations with it so it would be very helpful.

Thanks!

2

Dear @horlust,

The autocorrelation function of a set of data can still be calculated by the gmx analyze tool. Regarding the hbonds, you can use the old version of gmx hbond in GROMACS 2024 by using the gmx hbond-legacy tool which has the flags you need.