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:
Contact person:
Arun Sridhar — 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.