In this paper, we develop the formalism of entangled trajectory molecular dynamics (ETMD), introduced by Donoso and Martens [Phys. Rev. Lett. 2001, 87, 223202] in a form applicable to the treatment of general (i.e., nonpolynomial) potentials. We formulate our approach directly in terms of the integrodifferential equation obeyed by the Wigner function, without assuming a Taylor series expansion of the potential in powers of the coordinate. This alternative formalism has distinct advantages for propagating distribution functions represented by finite trajectory ensembles and for nonpolynomial potentials. We use a numerical implementation of the new approach to calculate the reaction probabilities for three model systems: the cubic polynomial potential, symmetric Eckart barrier and asymmetric Eckart barrier. Our results are in excellent agreement with the results of exact quantum calculation.