How to access the trajectory files

Requirements

• VMD 1.9.4

Instructions

1. Load a single PDB setup file, then the corresponding DCD trajectory file into VMD by clicking New Molecule > Browse > [find the PDB in file explorer] > Load > [find the DCD in file explorer] > Load
2. Click Graphics, then type "bonded not water" in the Selected Atoms textbox to only view the non-water molecules.
3. For ease of use, click on the trajectory tab, and change Trajectory Smoothing to 15 and Representations to Bonds.