Hydrogen-bond dynamics: the Auto Correlation Function

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1

Does lammps calculate the autocorrelation function for hydrogen bonds in the system? It is a very useful parameter that tells about the stability and dynamics of H-bonds.

It seems that Gromacs does it:
http://manual.gromacs.org/programs/gmx-hbond.html

Example References:

1- Alenka Luzar and David Chandler “Hydrogen-bond kinetics in liquid water”, Nature 379, 55 - 57.

2- Sungho Han, Pradeep Kumar and H. Eugene Stanley “Hydrogen-bond dynamics of water in a quasi-two-dimensional hydrophobic nanopore slit”, Phys. Rev. E 79, 041202, 2009.

2

Does lammps calculate the autocorrelation function for hydrogen bonds in the
system? It is a very useful parameter that tells about the stability and

no. nobody has programmed it. feel free to do it yourself and
contribute the code. that is how many parts of LAMMPS happened.

dynamics of H-bonds.

It seems that Gromacs does it:
http://manual.gromacs.org/programs/gmx-hbond.html

but you'll also see, if you look closer, that it is done in
post-processing. so if you set up things right and act smart, you can
use the gromacs tools to do the postprocessing of the LAMMPS
trajectories (of course, you could also just use gromacs all the way).

axel.