NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Supercomputing '96 Proceedings of the 1996 ACM/IEEE conference on Supercomputing
Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Blue matter on blue gene/L: massively parallel computation for biomolecular simulation
CODES+ISSS '05 Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis
Scalable algorithms for molecular dynamics simulations on commodity clusters
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Zonal methods for the parallel execution of range-limited N-body simulations
Journal of Computational Physics
Anton, a special-purpose machine for molecular dynamics simulation
Proceedings of the 34th annual international symposium on Computer architecture
Blue matter: scaling of N-body simulations to one atom per node
IBM Journal of Research and Development
Data mining for simulation algorithm selection
Proceedings of the 2nd International Conference on Simulation Tools and Techniques
Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
Parallel discrete event simulation with Erlang
Proceedings of the 1st ACM SIGPLAN workshop on Functional high-performance computing
Moving from petaflops to petadata
Communications of the ACM
Spin glass simulations on the janus architecture: a desperate quest for strong scaling
Euro-Par'12 Proceedings of the 18th international conference on Parallel processing workshops
Adaptive exploration for large-scale protein analysis in the molecular dynamics database
Proceedings of the 25th International Conference on Scientific and Statistical Database Management
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The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry, and medicine. A wide range of biologically interesting phenomena, however, occur over timescales on the order of a millisecond---several orders of magnitude beyond the duration of the longest current MD simulations. We describe a massively parallel machine called Anton, which should be capable of executing millisecond-scale classical MD simulations of such biomolecular systems. The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized highspeed communication network. Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation. The remainder of the simulation algorithm is executed by a programmable portion of each chip that achieves a substantial degree of parallelism while preserving the flexibility necessary to accommodate anticipated advances in physical models and simulation methods.