mdanalysis-trajectory

What problem does it solve?

This Skill simplifies the complex task of analyzing molecular dynamics (MD) simulation trajectories, allowing researchers to extract meaningful insights about molecular behavior over time.

Core Features & Use Cases

• Trajectory Loading: Uniformly load trajectories from various MD engines (GROMACS, AMBER, etc.).
• Structural Analysis: Calculate metrics like RMSD, RMSF, radius of gyration, and hydrogen bond occupancy.
• Conformational Analysis: Perform PCA to understand dominant modes of motion.
• Use Case: After running a molecular dynamics simulation of a protein-ligand complex, use this Skill to assess the stability of the ligand's binding pose by calculating its RMSD and analyzing hydrogen bond formation over time.

Quick Start

Use the mdanalysis-trajectory skill to load 'trajectory.xtc' and calculate the backbone RMSD.