FPGA MD code and data

This repository holds the implementation and simulation inputs scripts as well as some results for the papar "Molecular Dynamics Simulations Accelerated on FPGA with High-Bandwidth Memory".

Hardware Requirements

• Inspur F37X FPGA card

OS Required & Software Dependencies

• CentOS 7 (Kernal version 3.10.0)
• Vivado 2021.2
• GNU compiler >= 8.3.0
• OpenMM >= 6.0.0
• MDTraj

Build Instructions

C code: Use the Makefile in the tools to build the code.

VHDL and Verilog: Use Vivado to build the project.

Simulation inputs and outputs

Simulation inputs, outputs, analysis scripts are given in the simulations folder.
Further descriptions of these files are given in the README there.
Large size trajectories are provided at Zenodo:
MD Validation inputs and trajectories for "Molecular Dynamics Simulations Accelerated on FPGA with High-Bandwidth Memory" .