MDTraj

MDTraj reads and writes molecular dynamics trajectory data in a wide variety of commonly used formats and provides trajectory analysis capabilities that bridge MD data with the scientific Python ecosystem.

Key Features:

• Trajectory I/O: MDTraj reads and writes trajectory data in a wide variety of commonly used formats.
• Structural Analysis: MDTraj performs minimal root-mean-square-deviation calculations.
• Secondary Structure Assignment: MDTraj assigns secondary structure from trajectory data.
• Order Parameter Extraction: MDTraj extracts common order parameters from simulations.
• Python Ecosystem Interoperability: MDTraj bridges the gap between MD data and the scientific Python ecosystem for statistical analysis and visualization.

Scientific Applications:

• Molecular Dynamics Analysis: MDTraj analyzes molecular dynamics simulations of complex biomolecular systems.
• Biomolecular Structure Analysis: MDTraj calculates structural properties including root-mean-square-deviation and secondary structure from simulation trajectories.
• Order Parameter Analysis: MDTraj extracts common order parameters to characterize simulation dynamics.

Methodology:

MDTraj implements computational methods for reading and writing trajectory data, calculating minimal root-mean-square-deviation, assigning secondary structure, and extracting order parameters.