AmberAnalysis

A suite of command-line tools for analyzing chemically relevant features of an Amber Molecular Dynamics simulation. Can detect the position of a planar interface between two substances and plot density relative to that interface for atoms of an arbitrary type, name, charge, or residue. Orientation of three-atom residues (such as water) may be calculated and plotted. Uses parallel processing to detect hydrogen bonds, and can produce a bonding profile. Output files can be displayed as graphs using the included matplotlib python graphing script.