How are the atoms connected?

Every atom is connected to every other atom by a spring. With N atoms there are N times N minus 1 divided by 2 springs. So 3 atoms have 3 springs forming a triangle and 6 atoms have 15 springs forming a complex network.

What are vibrational modes?

With zero gravity and damping the molecule has distinct vibration patterns called normal modes. These include breathing modes where all atoms expand and contract together and rocking modes where the molecule tilts. These are the same modes measured by infrared spectroscopy in real molecules.

Molecule Simulator — N-Body Spring Dynamics

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Molecule Dynamics