Abstract: This paper reports a new GPU cluster system to meet the challenge of computing the protein molecular field by approaches of quantum chemistry.This system uses MPI(message passing interface)parallel programming environment to link all nodes of the cluster,adopts OpenMP(open multi-processing)as a multi-core CPU programming environment and CUDA as a GPU programming environment.We present an optimal parallel accelerating architecture to integrate multi-core CPU computation with GPU computation at each node of the GPU cluster system.By combining MPI,OpenMP and CUDA programming,it greatly speeds up the computation while maintaining high calculation precision.We tested the cluster system by calculating several protein molecular fields adhering to the theory of quantum chemistry.Compared with the previous approaches,such as CPU cluster,single GPU and single CPU,the proposed GPU cluster improves the calculation efficiency greatly.One example shows 7.5 times acceleration by employing the GPU cluster system in comparison with that by a corresponding CPU cluster.It is therefore capable of simulating the complex protein molecular field at high resolution.