MDScale: Scalable multi-GPU bonded and short-range molecular dynamics

•We propose and implement a bonded and short-range scalable molecular dynamics for distributed Multi-GPU environments.•Our approach makes the calculations of all forces completely in GPUs.•The algorithms, CUDA kernels and MPI communication are designed to improve scalability and runtime performance.•We test its scalability compared to NAMD by simulating on Amazon Web Services using both K80 and V100 GPUs.•We obtain linear horizontal scalability in multiple scenarios, including simulations of 1 billion atom molecules.