# hbonds autocorrelation  using GROMACS

**URL:** <https://gromacs.bioexcel.eu/t/hbonds-autocorrelation-using-gromacs/13660>\
**Category:** Third party tools and files\
**Tags:** analysis-tools\
**Created:** [August 11, 2026, 5:20pm UTC](https://gromacs.bioexcel.eu/t/hbonds-autocorrelation-using-gromacs/13660 "2026-08-11T17:20:19Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![askforarun](https://avatars.discourse-cdn.com/v4/letter/a/c5a1d2/32.png) [@askforarun](https://gromacs.bioexcel.eu/u/askforarun)\
**Post date:** [August 11, 2026, 5:20pm UTC](https://gromacs.bioexcel.eu/t/hbonds-autocorrelation-using-gromacs/13660/1 "2026-08-11T17:20:19Z")

</div>

Python tool for calculating hydrogen-bond autocorrelation functions from GROMACS `gmx hbond -pf` output. It calculates both intermittent and continuous hydrogen-bond autocorrelation functions and supports user-defined lag times and time-origin averaging. The tool is general and can be applied to any suitable GROMACS molecular-dynamics system.

**Link:**

> **[GitHub - askforarun/hbonds\_gromacs: Hydrogen-bond existence autocorrelation functions...](https://github.com/askforarun/hbonds_gromacs)**
>
> Hydrogen-bond existence autocorrelation functions from GROMACS gmx hbond -pf output, using GROMACS's own frame-by-frame bonded record with no geometric re-evaluation. Implements the Luzar-Chandler intermittent and continuous conventions. NumPy only.

**Contact person:**  
Arun Sridhar — [askforarun@gmail.com](mailto:askforarun@gmail.com)

The implementation has been tested using numerical and physical-invariant tests, error-handling tests, and a representative example dataset. The calculated autocorrelation functions are based on established intermittent and continuous hydrogen-bond correlation definitions, using the hydrogen-bond assignments generated directly by GROMACS.