Parallel Processor Design and Implementation for Molecular Dynamics Simulations on a FPGA-Based Supercomputer

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Journal of Computers

• Publication date

  2012-01-06

• Fields of study

  Computer Science, Engineering

• Identifiers
  DOI 10.4304/jcp.7.6.1312-1328
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Prediction of Protein Structure and the Principles of Protein Conformation

  2012cited by this paper
• Efficient particle-pair filtering for acceleration of molecular dynamics simulation

  2009cited by this paper
• Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations

  2008cited by this paper
• Accelerating Molecular Dynamics Simulations with Reconfigurable Computers

  2008cited by this paper
• The PowerPoint presentation

  2007cited by this paper
• The FPGA High-Performance Computing Alliance Parallel Toolkit

  2007cited by this paper
• Maxwell - a 64 FPGA Supercomputer

  2007cited by this paper
• A case study in porting a production scientific supercomputing application to a reconfigurable computer

  2006cited by this paper
• Improved Interpolation and System Integration for FPGA-Based Molecular Dynamics Simulations

  2006cited by this paper
• GROMACS: Fast, flexible, and free

  2005cited by this paper
• Scalable molecular dynamics with NAMD

  2005cited by this paper
• Accelerating molecular dynamics simulations with configurable circuits

  2005cited by this paper
• Computing Lennard-Jones Potentials and Forces with Reconfigurable Hardware

  2004cited by this paper
• A fully synthesizable single-precision, floating-point adder/substractor and multiplier in VHDL for general and educational use

  2004cited by this paper
• Reconfigurable molecular dynamics simulator

  2004cited by this paper
• A Preliminary Study of Molecular Dynamics on Reconfigurable Computers

  2003cited by this paper
• Development of MD Engine: High‐speed accelerator with parallel processor design for molecular dynamics simulations

  1999cited by this paper
• Particle-Mesh Ewald and rRESPA for Parallel Molecular Dynamics Simulations

  1997cited by this paper
• Fast and accurate molecular dynamics simulation of a protein using a special‐purpose computer

  1997cited by this paper
• The Art of Molecular Dynamics Simulation

  1997cited by this paper
• The art of molecular dynamics simulation

  1996cited by this paper
• The first step in sugar transport: crystal structure of the amino terminal domain of enzyme I of the E. coli PEP: sugar phosphotransferase system and a model of the phosphotransfer complex with HPr.

  1996cited by this paper
• A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase

  1996cited by this paper
• Solution structure of the donor site of a trans-splicing RNA.

  1996cited by this paper
• Fitting an inhibitor into the active site of thermolysin: A molecular dynamics case study

  1996cited by this paper
• A Highly Parallelized Special-Purpose Computer for Many-Body Simulations with an Arbitrary Central Force: MD-GRAPE

  1996cited by this paper
• Error evaluation in the design of a special‐purpose processor that calculates nonbonded forces in molecular dynamics simulations

  1995cited by this paper
• Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems

  1995cited by this paper
• Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

  1993cited by this paper
• Fast parallel algorithms for short-range molecular dynamics

  1993cited by this paper
• Reversible multiple time scale molecular dynamics

  1992cited by this paper
• Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions

  1992cited by this paper
• Prediction of protein structure and the principles of protein conformation

  1990cited by this paper
• Computer simulation of liquids

  1989cited by this paper
• A fast algorithm for particle simulations

  1987cited by this paper
• Some Multistep Methods for Use in Molecular Dynamics Calculations

  1976cited by this paper
• Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules

  1967cited by this paper
• Computer Simulation Using Particles

  1966cited by this paper
• Die Berechnung optischer und elektrostatischer Gitterpotentiale

  year unknowncited by this paper

• Toward an FPGA-based dedicated computer for molecular dynamics simulations.

  2025cites this paper
• Methodology of Firmware Development for ARUZ—An FPGA-Based HPC System

  2020cites this paper
• ARUZ - Large-scale, massively parallel FPGA-based analyzer of real complex systems

  2018cites this paper
• On the Feasibility of FPGA Acceleration of Molecular Dynamics Simulations

  2018cites this paper
• Redesigning LAMMPS for Peta-Scale and Hundred-Billion-Atom Simulation on Sunway TaihuLight

  2018cites this paper
• An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL

  2017cites this paper
• Molecular Dynamics Simulation of Iron — A Review

  2015cites this paper
• МОДЕЛИРОВАНИЕ ВЗАИМОДЕЙСТВИЙ БЕЛКОВ ФОТОСИНТЕТИЧЕСКОЙ ЭЛЕКТРОН-ТРАНСПОРТНОЙ ЦЕПИ ФОТОСИНТЕЗА МЕТОДОМ БРОУНОВСКОЙ ДИНАМИКИ

  2015cites this paper
• Implementation of Multi-channel FIFO in One BlockRAM with Parallel Access to One Port

  2014cites this paper
• Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer

  2014cites this paper
• Brake Pedal Displacement Measuring System based on Machine Vision

  2013cites this paper
• Research of ArtemiS in a Ring-Plate Cycloid Reducer

  2012cites this paper