In this paper, we develop the optimal source precoding matrix and relay amplifying matrices for non-regenerative multiple-input multiple-output (MIMO) relay communication systems with parallel relay nodes using the projected gradient (PG) approach. We show that the optimal relay amplifying matrices have a beamforming structure. Exploiting the structure of relay matrices, an iterative joint source and relay matrices optimization algorithm is developed to minimize the mean-squared error (MSE) of the signal waveform estimation at the destination using the PG approach. The performance of the proposed algorithm is demonstrated through numerical simulations.