AbstractForce field-based classical molecular dynamics (CMD) is efficient but its potential energy surface (PES) prediction error can be very large. Density functional theory (DFT)-based ab-initio molecular dynamics (AIMD) is accurate but computational cost limits its applications to small systems. Here, we propose a molecular dynamics (MD) methodology which can simultaneously achieve both AIMD-level high accuracy and CMD-level high efficiency. The high accuracy is achieved by exploiting deep neural network (DNN)’s arbitrarily-high precision to fit PES. The high efficiency is achieved by deploying multiplication-less DNN on a carefully-optimized special-purpose non von Neumann (NvN) computer to mitigate the performance-limiting data shuttling (i.e., ‘memory wall bottleneck’). By testing on different molecules and bulk systems, we show that the proposed MD methodology is generally-applicable to various MD tasks. The proposed MD methodology has been deployed on an in-house computing server based on reconfigurable field programmable gate array (FPGA), which is freely available at http://nvnmd.picp.vip.