For many classes of symplectic manifolds, the Hamiltonian flow of a function with sufficiently large variation must have a fast periodic orbit. This principle is the base of the notion of Hofer-Zehnder capacity and some other symplectic invariants and leads to numerous results concerning existence of periodic orbits of Hamiltonian flows. Along these lines, we show that given a negatively curved manifold M, a neighbourhood U-R of M in T*M, a sufficiently C-1-small magnetic field sigma and a non-trivial free homotopy class of loops alpha, then the magnetic flow of certain Hamiltonians supported in U-R with big enough minimum, has a one-periodic orbit in alpha. As a consequence, we obtain estimates for the relative Hofer-Zehnder capacity and the Biran-Polterovich-Salamon capacity of a neighbourhood of M.