I thought the Hamiltonian was always equal to the total energy of a system but have read that this isn't always true. Is there an example of this and does the Hamiltonian have a physical interpretation in such a case?
Answer
In an ideal, holonomic and monogenic system (the usual one in classical mechanics), Hamiltonian equals total energy when and only when both the constraint and Lagrangian are time-independent and generalized potential is absent.
So the condition for Hamiltonian equaling energy is quite stringent. Dan's example is one in which Lagrangian depends on time. A more frequent example would be the Hamiltonian for charged particles in electromagnetic field $$H=\frac{\left(\vec{P}-q\vec{A}\right)^2}{2m}+q\varphi$$ The first part equals kinetic energy($\vec{P}$ is canonical, not mechanical momentum), but the second part IS NOT necessarily potential energy, as in general $\varphi$ can be changed arbitrarily with a gauge.
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