A fast algorithm for particle simulations
Journal of Computational Physics
Computer simulation of liquids
Computer simulation of liquids
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Scalable atomistic simulation algorithms for materials research
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
An 8.61 Tflop/s molecular dynamics simulation for NaCl with a special-purpose computer: MDM
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
FPGAs vs. CPUs: trends in peak floating-point performance
FPGA '04 Proceedings of the 2004 ACM/SIGDA 12th international symposium on Field programmable gate arrays
Time-Critical Software Deceleration in an FCCM
FCCM '04 Proceedings of the 12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Reconfigurable Molecular Dynamics Simulator
FCCM '04 Proceedings of the 12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 3 - Volume 04
An Analysis of the Double-Precision Floating-Point FFT on FPGAs
FCCM '05 Proceedings of the 13th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Hardware/Software Approach to Molecular Dynamics on Reconfigurable Computers
FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Exploiting hierarchical parallelisms for molecular dynamics simulation on multicore clusters
The Journal of Supercomputing
Proceedings of the 8th ACM International Conference on Computing Frontiers
Scalability study of molecular dynamics simulation on Godson-T many-core architecture
Journal of Parallel and Distributed Computing
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Scientific computing is marked by applications with very high performance demands. As technology has improved, reconfigurable hardware has become a viable platform to provide application acceleration, even for floating-point-intensive scientific applications. Now, reconfigurable computers---computers with general purpose microprocessors, reconfigurable hardware, memory, and high performance interconnect---are emerging as platforms that allow complete applications to be partitioned into parts that execute in software and parts that are accelerated in hardware. In this paper, we study molecular dynamics simulation. Specifically, we study the use of the smooth particle mesh Ewald technique in a molecular dynamics simulation program that takes advantage of the hardware acceleration capabilities of a reconfigurable computer. We demonstrate a 2.7-2.9xspeed-up over the corresponding software-only simulation program. Along the way, we note design issues and techniques related to the use of reconfigurable computers for scientific computing in general.