Hydrogen bond analysis

This is a demonstration of using several recently added features to LAMMPS.

The simulation is based on the peptide example and uses the following added features:

• compute hbond/local to determine and visualize the hydrogen bonds between the peptide and the surrounding water molecules
• dynamic region keywords within and include to select only whole water molecules that are close enough to the peptide for a cleaner visualization
• fix graphics/labels to display the hydrogen bond counts and import the image with the hydrogen bond geometry schema
• fix graphics/objects to add the two arrows to the image to indicate which color arrow is a hydrogen bond donated or accepted by the peptide

For more information, see the LAMMPS Visualization Howto.