01
See the structure change.
Orbit a full-atom molecular viewer, switch representations, isolate residues, tune surfaces, and move frame by frame.
MOLECULAR DYNAMICS, REIMAGINED / 001
Make molecular motion visible.
A fluid home for trajectories, protein structure, and the science behind every frame. Explore the molecule and its analyses in one connected workspace.
Local-first by designLinux first release
REAL DEMO / STRUCTURE4,640 atoms
290 residues
real protein topology
real protein topology
Frame 0
source index / 5,000
source index / 5,000
DRAG TO ORBITPROTEIN CARTOON / PREVIEW
01continuous workspace
2D + 3Dlinked scientific views
Localyour data stays on your machine
Real datademo you can inspect
01 / THE WORKSPACE
The molecule and the meaning.
Always in sync.
A single place to move from structure to signal. Try a small preview computed from VisualMD’s bundled trajectory.
V•M visualmd explore REAL DEMO PREVIEW290 residues 5,001 source frames
PROTEIN VIEWER
Real protein. Real motion.Backbone cartoon from the bundled PDB/XTC pair
ANALYSIS STUDIO
CARTESIAN PROJECTION
LINKEDCollective motion
Each point is one retained frame. Select a frame below to locate it.
1× 50-frame preview
Interactive preview: 101 backbone cartoons sampled every 50 source frames, with secondary structure classified from the first frame. The analyses use all 1,001 stride-5 frames. Simulation protocol and equilibrium provenance are unspecified.
02 / WHAT'S INSIDE
Built to reveal
what a trajectory holds.
Visual tools with scientific context, so beautiful results remain interpretable.
02
Follow the motion.
Explore RMSD, RMSF, radius of gyration, contacts, DCCM, and linked 2D/3D PCA views.
03
Map the landscape.
Inspect projected free-energy estimates and sampled basin representatives, with interpretation limits kept visible.
04
Take the insight with you.
Export images, video, and data. Save a portable session when its inputs fit the current bundle limits.
03 / THE FLOW
From raw coordinates
to a clearer story.
One deliberate path through setup, analysis, and visual exploration.
Open
Bring a topology and trajectory, or start with the included real demo.
Prepare
Choose selection, frame stride, alignment, reference, and residue numbering.
Explore
Scrub the structure while linked plots bring relevant frames into view.
Share
Export visuals and results, with preparation details available for review.
04 / THE PRINCIPLE
Visual drama.
Scientific honesty.
VisualMD makes complex motion approachable while keeping selections, units, preprocessing choices, and interpretation limits close to the view.
- Original inputs are preserved.
- Frame identities stay traceable.
- Exploratory estimates are labelled clearly.
05 / FIRST RELEASE
The next frame
starts here.
VisualMD’s first downloadable release is being prepared for Linux. It will run the scientific workflow locally, with the real demo ready to explore.