RealQM — Molecular Dynamics

Real-time electron density computation on 3D grids using WebGPU compute shaders. Watch molecules assemble atom-by-atom, fold, and interact — from hydrogen to 1000-atom proteins.

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Requires WebGPU: Chrome 113+, Edge 113+, or Safari 17+. Large molecules need a modern GPU with ~1 GB memory.

Molecule — Interactive Simulation

Default simulation page with built-in atom placement. Start here.

Atom-by-Atom Grow Animations

Watch molecules assemble one atom at a time. Heavy skeleton builds first, then hydrogens, then solvent. Click "Add" or "Auto-grow" to control the process.

Water Cluster

9 atoms · 200³ grid
3 water molecules. Watch hydrogen bond network form.
growwater

Formamide

12 atoms · 200³ grid
H-CO-NH&sub2; — simplest peptide bond analog + 2 waters.
growsmall molecule

Ethanol

12 atoms · 200³ grid
CH&sub3;CH&sub2;OH + water. C-C-O skeleton first.
growsmall molecule

Glycine

16 atoms · 200³ grid
Simplest amino acid NH&sub2;-CH&sub2;-COOH + 2 waters.
growamino acid

Tri-Glycine Peptide

27 atoms · 300³ grid
NH&sub2;-Gly-Gly-Gly-COOH backbone + water.
growpeptide

Chignolin

~90 atoms · 300³ grid
10-residue mini-protein GYDPETGTWG at 50% fold.
growprotein

Hairpin β-sheet

~90 atoms · 300³ grid
12-residue glycine hairpin at 75% fold + water.
growprotein

Villin Headpiece

~999 atoms · 300³ grid
3-helix bundle (24 residues) + hydration shell. The big one.
growprotein

Small Molecules

Static electron density calculations. Fast convergence on 200³ grids.

H&sub2;

Hydrogen molecule
small molecule

H&sub2;O

Single water molecule
small moleculewater

CO&sub2;

Carbon dioxide
small molecule

NH&sub3;

Ammonia (3D geometry)
small molecule

H&sub2;CO

Formaldehyde
small molecule

HNO

Nitroxyl
small molecule

LiH

Lithium hydride
small molecule

Ethanol

CH&sub3;CH&sub2;OH
small molecule

Caffeine

C&sub8;H&sub1;&sub0;N&sub4;O&sub2; + water shell
small molecule

Camphor

C&sub1;&sub0;H&sub1;&sub6;O bicyclic terpenoid
small molecule

Molecules with Nuclear Dynamics

Electron density drives nuclear motion via Hellmann-Feynman forces. Press D to toggle dynamics.

H&sub2;O dynamics

Water with nuclear motion
dynamicswater

Glycine dynamics

Amino acid with nuclear motion
dynamicsamino acid

Caffeine dynamics

Caffeine with nuclear forces
dynamics

Ethanol dynamics

Ethanol with nuclear motion
dynamics

LiH dynamics

Lithium hydride stretching
dynamics

5 Water molecules

Small water cluster dynamics
dynamicswater

Peptides & Proteins

From single amino acids to 1000-atom three-helix bundles. 300³ grids.

Glycine

Single amino acid
amino acid

Ala dipeptide

Alanine dipeptide
peptide

Asp-Pro

Dipeptide with proline pyrrolidine ring
peptide

Hairpin

β-hairpin (folded)
protein

Hairpin slider

Adjustable fold fraction 0–100%
protein

Chignolin

10-residue mini-protein with fold slider
protein

Trp-cage

20-residue protein fold
protein

Villin headpiece

~1000 atoms, 3-helix bundle + hydration
protein

Water Clusters

3 waters

water

10 waters

water

50 waters

water

100 waters

water

1000 waters

Large-scale water simulation
water

Tools

Video Recorder

Record any grow animation as .webm video. Select molecule, set dwell time, press record.
recording

Bond length sweep

Scan energy vs bond distance.