How to Visualize Molecular Dynamics Trajectories in PyMOL: Animation, Key Frames and Export

Preparing the trajectory before loading

This step is the most commonly skipped — and the most important. Raw MD trajectories from GROMACS or AMBER contain artifacts from periodic boundary conditions: atoms appear to jump across the box boundary, the protein may be split across box edges, and solvent fills the entire simulation cell. Load a raw trajectory directly into PyMOL and you’ll see a fragmented, unrealistic structure.

Always process the trajectory before visualization. In GROMACS:

# Step 1: Fix periodic boundary — make molecule whole
gmx trjconv -s md.tpr -f md.xtc -o md_whole.xtc -pbc whole
# Select: Protein (or the molecule you want centered)

# Step 2: Center the protein, remove solvent for visualization
gmx trjconv -s md.tpr -f md_whole.xtc -o md_nojump.xtc \
    -center -pbc mol -ur compact
# Select: Protein (centering group), Protein (output group)

# Step 3 (optional): Reduce frames for easier visualization
# Keep every 10th frame (1 ns MD with 1 ps output → every 10 ns)
gmx trjconv -s md.tpr -f md_nojump.xtc -o md_vis.xtc -skip 10

Supported trajectory formats

Loading the topology and trajectory

PyMOL needs two files: a topology file (the structure — a GRO, PDB, or PSF) and the trajectory file. Load the topology first to create the object, then load the trajectory into that object.

# Method 1: load topology, then load trajectory into it
load protein.gro, protein            # creates the object "protein"
load_traj md_vis.xtc, protein        # loads frames into same object

# Method 2: load PDB topology, then XTC trajectory
load topology.pdb, my_sim
load_traj md_vis.xtc, my_sim

# Method 3: for multi-model PDB trajectories
load trajectory.pdb                  # each MODEL becomes one state/frame

# Load only a subset of frames (start, stop, step in frame numbers)
load_traj md_vis.xtc, protein, start=1, stop=100, step=5
# This loads frames 1-100, every 5th frame

# Check how many states (frames) were loaded
print(cmd.count_states("protein"))

After loading, set up your display — the same coloring and representation settings you’d use for a static structure apply equally to trajectory visualization. Set these before playing the trajectory so they persist across all frames:

as cartoon
hide everything, resn HOH
util.cbc
set cartoon_fancy_helices, 1
bg_color white

Playing back and navigating the trajectory

Once the trajectory is loaded, each frame is a separate “state” in PyMOL. Navigate between states using the playback controls at the bottom of the viewer window, or control playback entirely from the command line.

# Play trajectory
mplay

# Stop
mstop

# Jump to specific frame
frame 50

# Control playback speed (frames per second)
set movie_fps, 5    # slow — good for visualizing conformational detail
set movie_fps, 15   # medium — good for general animation
set movie_fps, 30   # fast — smooth video output

# Loop playback
set movie_loop, 1   # loop continuously (1=on, 0=off)

Making smooth animations

Raw trajectory playback can appear jerky — each frame is a distinct snapshot with no interpolation between them. PyMOL’s morph and smooth features interpolate between frames to produce fluid motion:

# Smooth the trajectory playback (interpolates between states)
smooth protein, 5    # 5 = smoothing window in frames
smooth protein, 10   # wider window = smoother, but loses fast dynamics

# Create a morph between two specific frames for a smooth conformational change
# (useful for showing a specific transition, not the whole trajectory)
create frame1, protein, 1    # extract frame 1 as separate object
create frame50, protein, 50  # extract frame 50 as separate object
morph morph_obj, frame1, frame50, refinement=5
# morph creates intermediate states between the two conformations

# Play the morph
mplay morph_obj

Capturing key frames

From a long trajectory, you often want to extract a handful of meaningful frames — the starting conformation, a key intermediate, and the end state. Extract them as static objects for comparison or publication figures:

# Extract specific frames as separate objects
create start_conf,  protein, 1      # frame 1 = starting conformation
create middle_conf, protein, 50     # frame 50 = mid-simulation
create end_conf,    protein, 100    # frame 100 = end conformation

# Save an extracted frame as a PDB file
frame 50
save frame50.pdb, protein, state=50

# Align all extracted frames to the starting conformation
super middle_conf, start_conf
super end_conf,    start_conf

# Color each conformation distinctly for comparison
color slate,     start_conf
color salmon,    middle_conf
color palegreen, end_conf

# Show all three together — conformational ensemble view
as cartoon
zoom

Showing conformational change

One of the most powerful things you can show from an MD trajectory is a specific conformational change — a loop opening, a domain rotating, a binding site changing shape. Two approaches work well in PyMOL:

Overlay approach — show multiple conformations simultaneously

# Extract start and end conformations
create open_state,   protein, 1
create closed_state, protein, 100

# Align on the stable core (not the region that changes)
select stable_core, resi 1-100 and name CA   # stable region
super closed_state and stable_core, open_state and stable_core

# Show both as cartoons with different colors
as cartoon
color slate,  open_state
color salmon, closed_state
set cartoon_transparency, 0.4, open_state  # ghost the reference state

# Highlight the region that moved
select mobile_region, resi 101-130
show sticks, mobile_region

Trail approach — show the path a residue takes

# Show Cα trace of a flexible loop across all trajectory frames
# First extract just the mobile region from all states
create loop_all, protein and resi 101-130 and name CA

# Show as spheres across all states — shows the range of motion
show spheres, loop_all
set sphere_scale, 0.3, loop_all
color orange, loop_all

Exporting as MP4 or GIF

# Step 1: Set up the movie — define frames and duration
mset 1 x100         # play states 1-100 once
mset 1 x100 1 -1 x100  # play forward then backward (boomerang loop)

# Step 2: Configure movie settings
set movie_fps, 15
bg_color white
set ray_opaque_background, 1
set cartoon_fancy_helices, 1

# Step 3: Export as PNG frames then encode with ffmpeg
mpng /tmp/frame_, ray=0   # export each state as PNG (ray=0 for speed)
# Then in terminal: ffmpeg -r 15 -i /tmp/frame_%04d.png -c:v libx264 -pix_fmt yuv420p movie.mp4

# Alternative: PyMOL's built-in movie export (educational/commercial license)
movie.produce movie.mp4, mode=normal, fps=15, quality=90

# Export frames as PNGs, then assemble GIF with ImageMagick (free)
mpng /tmp/frame_, ray=0
# In terminal:
# convert -delay 6 -loop 0 /tmp/frame_*.png animation.gif
# -delay 6 = ~16 fps (delay in 1/100 seconds)
# -loop 0 = loop forever

# Optimize GIF file size
# gifsicle --optimize=3 animation.gif -o animation_opt.gif