Abstract: In molecular dynamics simulation systems, the computation of range-limited forces between molecules requires frequent transfers and large amounts of particle data access. To reduce the computational load on the CPU, FPGAs can be used to accelerate the computation. However, in the FPGA-based molecular dynamics simulation system, the range-limited force calculation module faces huge data transfer pressure and access conflict problems. To address these problems, an interactive control system is designed based on the limited hardware resources on FPGAs. The system consists of a fetch control module and a particle data parsing module. The whole system achieves fast and reliable transmission of particle data from on-chip storage to the range-limited force calculation module through reasonable data arrangement and cooperative work of the two modules. The effectiveness and reliability of the system in processing particle data are further verified by hardware simulation and board-level experiments.

Key words: molecular dynamics, range-limited force, interactive control system, Field Programmable Gate Array （ FPGA）, parallel computing