Video 1 of 3
Water formation from H₂ + O₂
Hydrogen and oxygen molecules collide, their bonds break, and the atoms recombine into water. The simulation shows the rearrangement that the balanced equation hides.
2 H₂ + O₂ → 2 H₂O
The app
What is FAMPLE Molecular Dynamics?
FAMPLE Molecular Dynamics is a molecular dynamics (MD) application for exploring chemical reactions. You build a starting set of molecules, set the conditions, and let the simulation run. At every time step the app computes the forces between atoms and moves them according to Newton's laws of motion.
Because bonds are allowed to break and form during the run, the simulation does more than show molecules vibrating. It can show a real reaction pathway: which atoms meet first, which bonds give way, and how the product molecule ends up assembled. That makes FAMPLE a useful tool for teaching and for building intuition about reaction mechanisms.
How it works
From starting molecules to products
Set up the system
Place the reactant molecules in the simulation box with their atoms, bonds and starting positions.
Compute forces
At each time step the app evaluates the forces every atom feels from its neighbours.
Integrate motion
Positions and velocities are advanced in tiny femtosecond-scale steps, producing a trajectory.
Watch the reaction
Bonds break and form as atoms collide, and the trajectory is rendered as an animation you can follow.
Videos
Reactions simulated with FAMPLE Molecular Dynamics
Three reactions, each run as a molecular dynamics simulation.
Video 2 of 3
Diels-Alder reaction
A conjugated diene and a dienophile join in a [4+2] cycloaddition. Two new carbon–carbon sigma bonds form in one concerted step, closing a six-membered ring.
diene + dienophile → cyclohexene ring
Video 3 of 3
Lactide from two lactic acid molecules
Two lactic acid molecules condense into lactide, a cyclic diester, releasing water. Lactide is the monomer used to make polylactic acid (PLA), a common biodegradable plastic.
2 C₃H₆O₃ → C₆H₈O₄ + 2 H₂O