At the molecular scale, reactions happen when two molecules collide with enough energy and the right orientation — temperature sets how often that happens.
P(react | collision) = p_react
<v> ~ sqrt(T) (kinetic theory)
- Molecule A / B count — population of each species free-flying inside the periodic-ish simulation box.
- Collision reactivity — probability that a close encounter between A and B produces product C.
- Temperature — scales molecular speed, so hotter runs mean more collisions per second.
- Product formed — cumulative count of successful A+B→C conversions since the last reset.
Real molecular-dynamics software (GROMACS, LAMMPS) integrates Newton's equations for millions of atoms; this sim shows the same collide-and-react logic at a scale you can watch.