On the basis of the antisymmetrized molecular dynamics (AMD) of wave packets for the quantum system, a novel model (called AMD-V) is constructed by the stochastic incorporation of the diffusion and the deformation of wave packets which is calculated by Vlasov equation without any restriction on the one-body distribution. In other words, the stochastic branching process in molecular dynamics is formulated so that the instantaneous time evolution of the averaged one-body distribution is essentially equivalent to the solution of Vlasov equation. Furthermore, as usual molecular dynamics, AMD-V keeps the many-body correlation and can naturally describe the fluctuation among many channels of the reaction. It is demonstrated that the newly introduced process of AMD-V has drastic effects in heavy ion collisions of 40Ca + 40Ca at 35 MeV/nucleon, especially on the fragmentation mechanism, and AMD-V reproduces the fragmentation data very well. Discussions are given on the interrelation among the frameworks of AMD, AMD-V and other microscopic models developed for the nuclear dynamics.