Molecular dynamics (MD) simulates particle-level interactions in physical systems using Newtonian mechanics over discrete timesteps, offering deep insight into biological structures and behaviors. While MD maps well to parallel architectures, the dense short-range interactions, such as the Lennard-Jones potential, make efficient hardware implementation challenging. In this project, we optimize MD for FPGA by designing a parameterizable, ring-connected architecture that balances performance, resource usage, and routing simplicity.
Prerequisites
- Vitis 2023.1
- Network Layer build file
- Memory Mapped build files
- Source files
To build the simulator, run make. Please give up to 24 hours as the build time is quite significant to match timing and minimize wire congestion and resource usage.
To run the simulator, run python run.py.
To visualize the data, run viz.py.
