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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.
Features
- Calculate density of any residue along an arbitrary axis of the simulation.
- Calculate the position of a planar interface between two groups of residues on an arbitrary axis.
- Compute orientation of three-atom molecules.
- Compute hydrogen bonds.
- Produce a bonding profile.
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