Improved Random Batch Ewald Method in Molecular Dynamics Simulations.

Abstract

The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano/microscale. The method shows great potential to solve the computational bottleneck of long-range interactions, motivating a necessity to accelerate short-range components of the nonbonded interactions for a further speedup of MD simulations. In this work, we present an improved RBE method for the nonbonding interactions by introducing the random batch idea to constructing neighbor lists for the treatment of both the short-range part of the Ewald splitting and the Lennard-Jones potential. The efficiency that the novel neighbor list algorithm owes to the stochastic minibatch strategy can significantly reduce the total number of neighbors. We obtain the error estimate and convergence by theoretical analysis and implement the improved RBE method in the LAMMPS package. Benchmark simulations are performed to demonstrate the accuracy and stability of the algorithm. Numerical tests on computer performance by conducting large-scaled MD simulations for systems including up to 0.1 billion water molecules are run on massive clusters with up to 50000 CPU cores, demonstrating the attractive features such as the high parallel scalability and memory-saving of the method in comparison to the existing methods.