Filters








657 Hits in 5.1 sec

Incorporating flexibility in Anton, a specialized machine for molecular dynamics simulation

Jeffrey S. Kuskin, Cliff Young, J.P. Grossman, Brannon Batson, Martin M. Deneroff, Ron O. Dror, David E. Shaw
2008 High-Performance Computer Architecture  
Achieving this balance was a significant challenge in the design of Anton, a parallel machine that will accelerate MD simulations by several orders of magnitude.  ...  An effective special-purpose supercomputer for molecular dynamics (MD) requires much more than high-performance acceleration of computational kernels: such accelerators must be balanced with general-purpose  ...  Acknowledgments The authors wish to extend their thanks to Ken Mackenzie for valuable contributions to the work reported in this paper, and to Matthew Farrens and the anonymous reviewers for their insightful  ... 
doi:10.1109/hpca.2008.4658651 dblp:conf/hpca/KuskinYGBDDS08 fatcat:4nsazah77rd2heexl47hdoueue

Anton: A Specialized Machine for Millisecond-Scale Molecular Dynamics Simulations of Proteins

David E. Shaw
2009 2009 19th IEEE Symposium on Computer Arithmetic  
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle lead to important scientific advances and provide a powerful  ...  Our research group has recently completed a specialized, massively parallel machine called Anton, which is capable of calculating millisecond-scale molecular trajectories at an atomic level of detail.  ...  The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle lead to important scientific advances and provide a powerful  ... 
doi:10.1109/arith.2009.33 dblp:conf/arith/Shaw09 fatcat:n3v5nylpcncore63kgrlz3ikxy

Anton, a special-purpose machine for molecular dynamics simulation

David E. Shaw, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. Grossman, C. Richard Ho, Douglas J. Lerardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Martin M. Deneroff (+15 others)
2008 Communications of the ACM  
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 high-speed 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.  ...  CONCLUSION We have designed, and are currently in the process of implementing, a specialized, massively parallel machine, called Anton, for the high-speed execution of molecular dynamics simulations.  ... 
doi:10.1145/1364782.1364802 fatcat:fhohu3mfmzddjcqq4hwt3i76cy

Anton, a special-purpose machine for molecular dynamics simulation

David E. Shaw, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. Grossman, C. Richard Ho, Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Martin M. Deneroff (+15 others)
2007 Proceedings of the 34th annual international symposium on Computer architecture - ISCA '07  
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 high-speed 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.  ...  CONCLUSION We have designed, and are currently in the process of implementing, a specialized, massively parallel machine, called Anton, for the high-speed execution of molecular dynamics simulations.  ... 
doi:10.1145/1250662.1250664 dblp:conf/isca/ShawDDKLSYBBCEGGHIKKLMMMPSSTTW07 fatcat:lfa6hizfi5cwhj3rznaf32vlmm

Anton, a special-purpose machine for molecular dynamics simulation

David E. Shaw, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. Grossman, C. Richard Ho, Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Martin M. Deneroff (+15 others)
2007 SIGARCH Computer Architecture News  
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 high-speed 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.  ...  CONCLUSION We have designed, and are currently in the process of implementing, a specialized, massively parallel machine, called Anton, for the high-speed execution of molecular dynamics simulations.  ... 
doi:10.1145/1273440.1250664 fatcat:lygdje54hnca5an6lwjfppn22u

Extending the Generality of Molecular Dynamics Simulations on a Special-Purpose Machine

Daniele P. Scarpazza, Douglas J. Ierardi, Adam K. Lerer, Kenneth M. Mackenzie, Albert C. Pan, Joseph A. Bank, Edmond Chow, Ron O. Dror, J.P. Grossman, Daniel Killebrew, Mark A. Moraes, Cristian Predescu (+2 others)
2013 2013 IEEE 27th International Symposium on Parallel and Distributed Processing  
We have previously described a massively parallel special-purpose supercomputer, called Anton, and have shown that it executes traditional molecular dynamics simulations orders of magnitude faster than  ...  Even within a single application area, however, a special-purpose machine can be far more valuable if it is capable of efficiently supporting a number of different computational methods that, taken together  ...  While Anton is specialized for molecular dynamics, a similar combination of hardware and software design strategies may be useful in accommodating a diverse set of methods on machines designed for other  ... 
doi:10.1109/ipdps.2013.93 dblp:conf/ipps/ScarpazzaILMPBCDGKMPSS13 fatcat:wg7jtjrhtfg3xf2tpxnuxk57j4

Millisecond-scale molecular dynamics simulations on Anton

David E. Shaw, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Douglas J. Ierardi, John L. Klepeis, Jeffrey S. Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Ron O. Dror (+10 others)
2009 Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis - SC '09  
ABSTRACT Anton is a recently completed special-purpose supercomputer designed for molecular dynamics (MD) simulations of biomolecular systems.  ...  Figure 1 : Two renderings of a protein (BPTI) taken from a molecular dynamics simulation on Anton.  ...  software and test infrastructure; Tiankai Tu for helpful comments on the paper; and Rebecca Kastleman and Jennifer McGrady for editorial assistance.  ... 
doi:10.1145/1654059.1654126 dblp:conf/sc/ShawDSGMBYDBBCEIKKLLMMPST09a fatcat:zn37hseoxveyxdmorr5joc5fj4

Overcoming Communication Latency Barriers in Massively Parallel Scientific Computation

Ron Dror, J.P. Grossman, Kenneth Mackenzie, Brian Towles, Edmond Chow, John Salmon, Cliff Young, Joseph Bank, Brannon Batson, David Shaw, Jeffrey S. Kuskin, Richard H. Larson (+2 others)
2011 IEEE Micro  
Acknowledgments We thank Ed Priest, Larry Nociolo, Chester Li, and Jon Peticolas for their work on high-speed analog circuits and signal integrity in Anton's communication channels; Stan Wang for design  ...  verification and validation; Amos Even for an array of system soft-  ...  6 Anton's speedup is partly attributable to the use of specialized hardware that greatly accelerates the arithmetic computation required for a molecular dynamics simulation.  ... 
doi:10.1109/mm.2011.38 fatcat:n5hkj2k53jforilvu23bt2bbly

High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation

Richard H. Larson, John K. Salmon, Ron O. Dror, Martin M. Deneroff, Cliff Young, J.P. Grossman, Yibing Shan, John L. Klepeis, David E. Shaw
2008 High-Performance Computer Architecture  
Anton is a massively parallel special-purpose supercomputer designed to accelerate molecular dynamics (MD) simulations by several orders of magnitude, making possible for the first time the atomic-level  ...  In Anton, such range-limited interactions are handled by a high-throughput interaction subsystem (HTIS).  ...  Acknowledgments The authors wish to extend their thanks to Joe Bank, Greg Lund and John Schomburg for valuable contributions to the work reported in this paper.  ... 
doi:10.1109/hpca.2008.4658650 dblp:conf/hpca/LarsonSDDYGSKS08 fatcat:vzkzlzv5freqhndfnypbynwv7m

Chemistry: Power play

Brendan Borrell
2008 Nature  
A new program called Desmond, he saw, could calculate each step of a standard moleculardynamics simulation -the 23,558 atoms in a system involving the protein dihydrofolate reductase -in a little over  ...  But the German-born physicist got his wakeup call in 2006, when he saw a table of computing benchmarks in a report from that year's supercomputing conference in Tampa, Florida.  ...  When Shaw began the work, he estimated that Anton would run molecular-dynamics simulations 1,000 times faster than previous parallel supercomputers.  ... 
doi:10.1038/451240a pmid:18202619 fatcat:wsqskef7hzclvjo5keuaosedqi

Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design

William Sinko, Steffen Lindert, J. Andrew McCammon
2012 Chemical Biology and Drug Design  
Protein flexibility plays a major role in biomolecular recognition. In many cases, it is not obvious how molecular structure will change upon association with other molecules.  ...  Here, we review a number of techniques that have been proposed to accommodate receptor flexibility in the simulation of small molecules binding to protein receptors.  ...  In addition, special purpose machines like Anton have been built for running fast MD simulations and extending brute force MD simulation into the millisecond timescale (36) .  ... 
doi:10.1111/cbdd.12051 pmid:23253130 pmcid:PMC3540989 fatcat:tso4kv2zqrfmndvfkekcw3f24a

Filtering, Reductions and Synchronization in the Anton 2 Network

J.P. Grossman, Brian Towles, Brian Greskamp, David E. Shaw
2015 2015 IEEE International Parallel and Distributed Processing Symposium  
We present three network features targeting this problem that have been implemented in Anton 2, a massively parallel special-purpose supercomputer for MD simulations.  ...  Parallel implementations of molecular dynamics (MD) simulation require significant inter-node communication, but off-chip communication bandwidth is not scaling as quickly as on-chip logic density.  ...  ACKNOLWEDGEMENTS We would like to thank Ken Mackenzie for assistance with performance experiments, and Mollie Kirk and Rebecca Bish-Cornelissen for editorial assistance.  ... 
doi:10.1109/ipdps.2015.42 dblp:conf/ipps/GrossmanTGS15 fatcat:xr7kevasjreonk2ixba4mm2bmi

Ensemble Docking in Drug Discovery

Rommie E. Amaro, Jerome Baudry, John Chodera, Özlem Demir, J. Andrew McCammon, Yinglong Miao, Jeremy C. Smith
2018 Biophysical Journal  
Ensemble docking corresponds to the generation of an "ensemble" of drug target conformations in computational structure-based drug discovery, often obtained by using molecular dynamics simulation, that  ...  This review gives a historical account of the development of ensemble docking and discusses some pertinent methodological advances in conformational sampling.  ...  The construction of special purpose computers, such as ANTON (16) , has allowed MD simulations of proteins to now be extended to the millisecond timescale.  ... 
doi:10.1016/j.bpj.2018.02.038 pmid:29606412 pmcid:PMC6129458 fatcat:6kyspe4scneenklkuotmzs7xhe

Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes

Jamie Parkin, Matthieu Chavent, Syma Khalid
2015 Biophysical Journal  
In the following review we use recent examples from the literature to discuss progress in the area of atomistic and coarse-grained molecular dynamics simulations of selected bacterial membranes and proteins  ...  of these membranes are now being incorporated into molecular-level models.  ...  ACKNOWLEDGMENTS The authors thank Mark Sansom and Prapasiri Pongprayoon for providing the data for Fig. 3 .  ... 
doi:10.1016/j.bpj.2015.06.050 pmid:26244728 pmcid:PMC4571018 fatcat:zvljbspgenc5pek2glkfwlona4

Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins

Hao Geng, Fangfang Chen, Jing Ye, Fan Jiang
2019 Computational and Structural Biotechnology Journal  
On the other hand, physics-based methods including molecular dynamics (MD) can utilize our understanding of detailed atomic interactions determining biomolecular structures.  ...  Then, some notable successes in reproducing experimental 3D structures of small proteins through MD simulations (some with replica-exchange) of the folding were summarized.  ...  Using Anton machine, Piana et al. performed eight onemillisecond (1 ms) MD simulations of ubiquitin (a very common 76residue protein) in explicit water [141] .  ... 
doi:10.1016/j.csbj.2019.07.010 pmid:31462972 pmcid:PMC6709365 fatcat:sezmyeefl5ezzh5ymqoiyz6hmm
« Previous Showing results 1 — 15 out of 657 results