From: Ern Ong (
Date: Tue Dec 06 2016 - 21:38:26 CST

Dear VMD users,

I have run a water simulation in LAMMPS and the output file format is .xyz, which does not include any bond and angle information. My question is whether this .xyz output file can be used to determine the number of hydrogen bonds in the simulation box? I have looked up VMD documentation and found this:

A possible hydrogen bond is defined by the following criteria:
Given an atom D with a hydrogen H bonded to it and an atom A with no hydrogen bonded to it, a hydrogen bond exists between A and H if the distance ||D-A|| < dist and the angle D-H-A < ang, where ang and dist are user defined.

Thank you.