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Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters

Kevin Bowers, Edmond Chow, Huafeng Xu, Ron Dror, Michael Eastwood, Brent Gregersen, John Klepeis, Istvan Kolossvary, Mark Moraes, Federico Sacerdoti, John Salmon, Yibing Shan (+1 others)
2006 ACM/IEEE SC 2006 Conference (SC'06)  
These methods are embodied in a newly developed MD code called Desmond that achieves unprecedented simulation throughput and parallel scalability on commodity clusters.  ...  Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain  ...  We also wish to thank the referees for their helpful suggestions.  ... 
doi:10.1109/sc.2006.54 fatcat:yx2ivaz25zfppabjumlm7wvp7m

Molecular dynamics recipes for genome research

Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza
2017 Briefings in Bioinformatics  
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles.  ...  even make the commodity hardware definitely suitable for MD studies.  ...  Introduction Molecular dynamics (MD) simulation is a leading tool of theoretical scientists for the study of the time-dependent motion of atoms and molecules.  ... 
doi:10.1093/bib/bbx006 pmid:28334084 fatcat:pw7hlvlfobea7hboz335p5wno4

Scalable molecular dynamics with NAMD

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten
2005 Journal of Computational Chemistry  
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.  ...  NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers.  ...  The authors would also like to acknowledge Fatemeh Khalili-Araghi and Marcos Sotomayor for preparing the ubiquitin tetramer and ubiquitin simulations. Free energy calculation development with C.  ... 
doi:10.1002/jcc.20289 pmid:16222654 pmcid:PMC2486339 fatcat:ltac7t3jtrbkngvn33tkmemmta

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 ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the most important currently  ...  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.  ...  This compares to a maximum benchmark parameter simulation rate of 14 ns/day for NAMD on our cluster (using 256 processor cores on 128 cluster nodes 3 ).  ... 
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 ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the most important currently  ...  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.  ...  This compares to a maximum benchmark parameter simulation rate of 14 ns/day for NAMD on our cluster (using 256 processor cores on 128 cluster nodes 3 ).  ... 
doi:10.1145/1273440.1250664 fatcat:lygdje54hnca5an6lwjfppn22u

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 ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the most important currently  ...  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.  ...  This compares to a maximum benchmark parameter simulation rate of 14 ns/day for NAMD on our cluster (using 256 processor cores on 128 cluster nodes 3 ).  ... 
doi:10.1145/1364782.1364802 fatcat:fhohu3mfmzddjcqq4hwt3i76cy

Performance characterization of molecular dynamics techniques for biomolecular simulations

Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwal, Al Geist
2006 Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming - PPoPP '06  
Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology.  ...  In this paper, we present detailed investigations of the performance issues, which are crucial for improving the scalability of the MD-related algorithms and applications on massively parallel processing  ...  (for access to Blue Gene/L).  ... 
doi:10.1145/1122971.1122983 dblp:conf/ppopp/AlamVAG06 fatcat:gb65colchrfmbiv4robentasdm

Interactive Molecular Dynamics: Scaling up to Large Systems

Matthieu Dreher, Marc Piuzzi, Ahmed Turki, Matthieu Chavent, Marc Baaden, Nicolas Férey, Sébastien Limet, Bruno Raffin, Sophie Robert
2013 Procedia Computer Science  
Combining molecular dynamics simulations with user interaction would have various applications in both education and research.  ...  In this paper, we propose an approach to combine a classical parallel molecular dynamics simulator, Gromacs, to a 3D virtual reality environment allowing to steer the simulation through external user forces  ...  Experiments were performed on the Grid'5000 experimental testbed (https://www.grid5000.fr).  ... 
doi:10.1016/j.procs.2013.05.165 fatcat:fedek7baivfprmuvgqnskxuwe4

Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques

H.M. Aktulga, J.C. Fogarty, S.A. Pandit, A.Y. Grama
2012 Parallel Computing  
Molecular dynamics modeling has provided a powerful tool for simulating and understanding diverse systems -ranging from materials processes to biophysical phenomena.  ...  Parallel formulations of these methods have been shown to be among the most scalable scientific computing applications. Many instances of  ...  Acknowledgment The authors would like to thank Adri van Duin for significant help through all aspects of software development, Aidan Thompson and Steve Plimpton for various discussions on parallel ReaxFF  ... 
doi:10.1016/j.parco.2011.08.005 fatcat:z6rvynvrbra7dmqtn3w52wcnoa

LARGE-SCALE MOLECULAR-DYNAMICS SIMULATION OF 19 BILLION PARTICLES

KAI KADAU, TIMOTHY C. GERMANN, PETER S. LOMDAHL
2004 International Journal of Modern Physics C  
We have performed parallel large-scale molecular-dynamics simulations on the QSCmachine at Los Alamos.  ...  These abilities pave the way for future atomistic large-scale simulations of physical problems with system sizes on the µ-scale.  ...  Kadau thanks Johannes Roth for many discussions on large-scale computing.  ... 
doi:10.1142/s0129183104005590 fatcat:46t2qntp5vcmjchvlbwbcycfbu

Parallel Molecular Dynamics with Irregular Domain Decomposition

Mauro Bisson, Massimo Bernaschi, Simone Melchionna
2011 Communications in Computational Physics  
AbstractThe spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel processing.  ...  Recent efforts aimed at simulating complex biological systems, like the blood flow inside arteries, require the execution of Parallel Molecular Dynamics (PMD) in vessels that have, by nature, an irregular  ...  Molecular dynamics Molecular Dynamics is a general term that indicates the numerical technique for the simulation of a wide range of physical phenomena, from the atomic to the cellular scale, in presence  ... 
doi:10.4208/cicp.140810.021210a fatcat:7tpnuewnvvccphkjlb3tgz674a

ACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale [article]

M. J. Harvey, G. Giupponi, G. De Fabritiis
2009 arXiv   pre-print
The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations.  ...  ACEMD is a production-class bio-molecular dynamics (MD) simulation program designed specifically for GPUs which is able to achieve supercomputing scale performance of 40 nanoseconds/day for all-atom protein  ...  MOLECULAR DYNAMICS ON THE GPUACEMD implements all features of an MD simulation on a CUDA-compatible GPU device, including those usually required for production simulations in the NVT ensemble (ie bonded  ... 
arXiv:0902.0827v1 fatcat:ldqlm4o4fnh3tcf54jzjbdynue

A scalable parallel algorithm for dynamic range-limitedn-tuple computation in many-body molecular dynamics simulation

Manaschai Kunaseth, Rajiv K. Kalia, Aiichiro Nakano, Ken-ichi Nomura, Priya Vashishta
2013 Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '13  
Recent advancements in reactive molecular dynamics (MD) simulations based on many-body interatomic potentials necessitate efficient dynamic n-tuple computation, where a set of atomic n-tuples within a  ...  Based on translation/reflection-invariant properties of computation patterns within this framework, we design a shiftcollapse (SC) algorithm for cell-based parallel MD.  ...  INTRODUCTION Molecular dynamics (MD) is a simulation method to study the dynamics of particles (e.g. atoms).  ... 
doi:10.1145/2503210.2503235 dblp:conf/sc/KunasethKNNV13 fatcat:sdwz6nierrbwvpfrt6gduvmw74

Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS [article]

Szilárd Páll, Artem Zhmurov, Paul Bauer, Mark Abraham, Magnus Lundborg, Alan Gray, Berk Hess, Erik Lindahl
2020 arXiv   pre-print
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using  ...  commodity hardware.  ...  In most cases molecular dynamics targeting a specific application depends critically on achieving faster simulations by reducing the time each MD step takes.  ... 
arXiv:2006.09167v2 fatcat:b6jiwmemtvbn3cz3mjfphbfeiu

New Born-Oppenheimer molecular dynamics based on the extended Hueckel method: first results and future developments [article]

Pedro E M Lopes
2018 arXiv   pre-print
In this publication the diagonalization problem is addressed and results from molecular dynamics simulations of alanine decamer in gas-phase using a new fast pseudo-diagonalization method are presented  ...  Computational chemistry at the atomic level has largely branched into two major fields, one based on quantum mechanics and the other on molecular mechanics using classical force fields.  ...  In 2006, for example, the first molecular dynamics simulation of a system with more than a million atoms was reported [9] .  ... 
arXiv:1810.07680v2 fatcat:le4z5ilj4fhnbfvdd3uzwji5oy
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