Tutorials

Selected tutorials and notes related to molecular dynamics, trajectory analysis, and visualization tools.

• MMPBSA calculation using .dcd trajectories

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  This tutorial walks through file conversion steps to generate GROMACS-compatible files for protein–ligand or protein–protein interaction free-energy calculations using g_mmpbsa, gmx mmpbsa, and related tools.

• Common trajectory analysis commands (GROMACS)

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  A concise reference of commonly used GROMACS commands for simulation trajectory analysis.

• Basic PyMOL tutorials for beginners

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  Introductory PyMOL tutorials covering basic visualization, selections, and rendering for structural biology.

• Thermodynamic Integration (fast growth)

  Notes and planned material on thermodynamic integration methods using fast-growth approaches. (Content to be expanded.)