Accelerating molecular dynamic simulation on the cell processor and Playstation 3

  title={Accelerating molecular dynamic simulation on the cell processor and Playstation 3},
  author={Edgar Luttmann and Daniel L. Ensign and Vaidyanathan Vishal and Mike Houston and Noam Rimon and Jeppe {\O}land and Guha Jayachandran and Mark S. Friedrichs and Vijay S. Pande},
  journal={Journal of Computational Chemistry},
Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing… 
High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing
The capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each is demonstrated, and GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers, is described.
The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis
The improved performance of modern simulation methods coupled with hardware advances is shifting the rate-limiting steps of common biomolecular simulations of small to moderately sized systems from the generation of data to the pre- and postprocessing phases of the workflow, namely, simulation setup and data processing, management, and analysis.
AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble
A GPLv2 implementation called AWE-WQ of a THE AUTHORS algorithm using the master/worker distributed computing WorkQueue (WQ) framework is provided, which is scalable to thousands of nodes and supports dynamic allocation of computer resources, heterogeneous resource usage, seamless heterogeneous cluster usage, and support for arbitrary MD codes such as GROMACS.
A Memory Centric Kernel Framework for Accelerating Short-Range, Interactive Particle Simulation
  • Ian Stewart, Shujia Zhou
  • Computer Science
    2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing
  • 2010
To maximize the performance of emerging multi- and many-core accelerators such as the IBM Cell B.E. and the NVIDIA GPU, a Memory Centric Kernel Framework (MCKF) was developed. MCKF allows a user to
An (almost) direct deployment of the Fast Multipole Method on the Cell processor
This paper presents the first deployment of the Fast Multipole Method on the Cell processor (PowerXCell 8i) in single and double precisions, which scales linearly on several Cell blades and which is able to handle both uniform and non-uniform distributions of particles.
Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.
This work introduces a new approach for learning a distance metric explicitly constructed to model kinetic similarity, which enables the construction of models, especially in the regime of high anisotropy in the diffusion constant, with fewer states than was previously possible.
Exploiting 162-Nanosecond End-to-End Communication Latency on Anton
  • R. Dror, J. P. Grossman, D. E. Shaw
  • Computer Science
    2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
  • 2010
Key elements of Anton's approach, in addition to tightly integrated communication hardware, include formulating data transfer in terms of counted remote writes, leveraging fine-grained communication, and establishing fixed, optimized communication patterns.


Accelerating molecular modeling applications with graphics processors
An overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techniques required to obtain optimal performance in these cases.
The Amber biomolecular simulation programs
The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build
GROMACS: Fast, flexible, and free
The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth‐permittivity finite difference Poisson–Boltzmann method
A fast stable finite difference Poisson–Boltzmann (FDPB) model for implicit solvation in molecular dynamics simulations was developed using the smooth permittivity FDPB method implemented in the
GROMACS 3.0: a package for molecular simulation and trajectory analysis
The design includes an extraction of virial and periodic boundary conditions from the loops over pairwise interactions, and special software routines to enable rapid calculation of x–1/2.
The potential of the cell processor for scientific computing
This work introduces a performance model for Cell and applies it to several key scientific computing kernels: dense matrix multiply, sparse matrix vector multiply, stencil computations, and 1D/2D FFTs, and proposes modest microarchitectural modifications that could significantly increase the efficiency of double-precision calculations.
Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation
A new classical empirical potential is proposed for water. The model uses a polarizable atomic multipole description of electrostatic interactions. Multipoles through the quadrupole are assigned to
Modification of the Generalized Born Model Suitable for Macromolecules
The analytic generalized Born approximation is modified to permit a more accurate description of large macromolecules, while its established performance on small compounds is nearly unaffected, and is adapted to describe molecules with an interior dielectric constant not equal to unity.