Create captivating simulation movies using the VMD Movie Maker tool.

Learn how to use VMD to effortlessly load, and visualize xtc files and molecular dynamics trajectories to understand the behavior of your system

A reference guide to every GROMACS file format: topology (.top), force-field parameters (.itp), coordinate files (.gro), run input (.tpr), trajectory (.xtc), and energy files (.edr). Understand what each file contains and when it is generated.

Learn to align protein structures in PyMOL using align, super, and cealign. Covers full-protein, chain, backbone, and ligand alignment with working examples.

A brief explanation of what is a PDB file, its importance in computational chemistry, and how it is formatted.

Render publication-quality images in PyMOL with the ray command. Covers ray trace modes, background color, transparent PNG export, and DPI settings.

Measure distances and angles in PyMOL with the distance command and Wizard. Includes cutoff filtering, polar contacts, and binding site interaction analysis.

Learn how to cluster frames in GROMACS using the gmx cluster command to find the most representative structure in your simulation.

Learn how to color molecules in PyMOL by chain, residue, secondary structure, or custom color schemes. Covers changing representations (cartoon, sticks, spheres), modifying the background color, and saving publication-quality images.

Master PyMOL selections: select atoms by residue number, chain, name, b-factor and proximity. Includes and, or, not operators with copy-paste examples.