  The implementation of Molecular Dynamics (MD) on FPGAs has received
substantial attention. Previous work, however, has consisted of either
proof-of-concept implementations of components, usually the range-limited
force; full systems, but with much of the work shared by the host CPU; or
prototype demonstrations, e.g., using OpenCL, that neither implement a whole
system nor have competitive performance. In this paper, we present what we
believe to be the first full-scale FPGA-based simulation engine, and show that
its performance is competitive with a GPU (running Amber in an industrial
production environment). The system features on-chip particle data storage and
management, short- and long-range force evaluation, as well as bonded forces,
motion update, and particle migration. Other contributions of this work include
exploring numerous architectural trade-offs and analysis on various mappings
schemes among particles/cells and the various on-chip compute units. The
potential impact is that this system promises to be the basis for long
timescale Molecular Dynamics with a commodity cluster.
