Playground

Temperature 0, potential energy per atom 0, time 0

Atoms interact through the Lennard-Jones potential. Classical force fields use the same pairwise term for van der Waals forces. Lower the temperature and the atoms condense into droplets and crystals. Raise it and they evaporate into a gas.

The simulation integrates Newton's equations with the velocity Verlet scheme and holds the temperature with a Berendsen thermostat, as real molecular dynamics codes do. It runs in reduced units and two dimensions. Colour shows speed, from slow in blue to fast in orange.

You can also run the same simulation on the server that hosts this site. Your browser then sends the current positions and velocities, and the server advances them by a few dozen steps and sends them back. This is a capability test for a small cloud machine, so expect it to be slower than your browser.

Steps per second in this browser, computation only

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Steps per second on the server, computation only

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Steps per second on the server, including network

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Server round trip

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Drag the molecule to rotate it. The 3D coordinates were generated with RDKit and optimised with the MMFF force field. These are the same first steps that prepare a ligand for docking.

Formula

Atoms

Carbon is grey, oxygen red, nitrogen blue and hydrogen white.

Eat the red dots and avoid the walls and your own tail. The snake speeds up as it grows.

Click or tap the board to start. Steer with the arrow keys, W A S D, or by swiping on the board. Space pauses.

Your best score is kept in this browser only.

Passwords are made in your browser with its cryptographic random number generator. They are never sent anywhere or stored.