Search results for "namd"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
93	Abhinav Bhatele, Sameer Kumar 0001, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kalé	Overcoming scaling challenges in biomolecular simulations across multiple platforms.	IPDPS	2008	DBLP DOI BibTeX RDF
93	Volodymyr V. Kindratenko, David Pointer	A case study in porting a production scientific supercomputing application to a reconfigurable computer.	FCCM	2006	DBLP DOI BibTeX RDF
78	Siegfried Benkner, Christian Schröder, Mária Lucká, Othmar Steinhauser	Grid Services for Parallel Molecular Dynamics with NAMD and CHARMM.	ICCSA (1)	2008	DBLP DOI BibTeX RDF	NAMD, CHARMM, ionic liquid, Grid service, molecular dynamics
65	Guochun Shi, Volodymyr V. Kindratenko	Implementation of NAMD molecular dynamics non-bonded force-field on the cell broadband engine processor.	IPDPS	2008	DBLP DOI BibTeX RDF
65	Sameer Kumar 0001, Chao Huang 0029, George Almási 0001, Laxmikant V. Kalé	Achieving strong scaling with NAMD on Blue Gene/L.	IPDPS	2006	DBLP DOI BibTeX RDF
56	Laxmikant V. Kalé, Sameer Kumar 0001, Gengbin Zheng, Chee Wai Lee	Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study.	International Conference on Computational Science	2003	DBLP DOI BibTeX RDF
47	Nancy Tran, Daniel A. Reed	Modeling of NAMD's Network Input/Output on Large PC Clusters.	IPDPS	2007	DBLP DOI BibTeX RDF
47	Rafal Kluszczynski, Piotr Bala	Supporting NAMD Application on the Grid Using GPE.	PPAM	2007	DBLP DOI BibTeX RDF
47	James C. Phillips, Gengbin Zheng, Sameer Kumar 0001, Laxmikant V. Kalé	NAMD: biomolecular simulation on thousands of processors.	SC	2002	DBLP DOI BibTeX RDF
37	Jason R. Villarreal, Walid A. Najjar	Compiled hardware acceleration of Molecular Dynamics code.	FPL	2008	DBLP DOI BibTeX RDF
31	Justin M. Wozniak, Michael Wilde	JETS: Language and System Support for Many-Parallel-Task Computing.	ICPP Workshops	2011	DBLP DOI BibTeX RDF	namd, mptc, mpi, many-task computing, mtc
31	Sadaf R. Alam, Jeffery A. Kuehn, Richard F. Barrett, Jeffrey M. Larkin, Mark R. Fahey, Ramanan Sankaran, Patrick H. Worley	Cray XT4: an early evaluation for petascale scientific simulation.	SC	2007	DBLP DOI BibTeX RDF	AORSA, Cray XT4, HPCC, IOR, NAMD, S3D, CAM, POP
28	Santiago Antolínez, Peter Eugene Jones, James C. Phillips, Jodi A. Hadden-Perilla	AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD.	J. Chem. Inf. Model.	2024	DBLP DOI BibTeX RDF
28	David J. Hardy, Jaemin Choi, Wei Jiang, Emad Tajkhorshid	Experiences Porting NAMD to the Data Parallel C++ Programming Model.	IWOCL	2022	DBLP DOI BibTeX RDF
28	Haochuan Chen, Julio D. C. Maia, Brian K. Radak, David J. Hardy, Wensheng Cai, Christophe Chipot, Emad Tajkhorshid	Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD.	J. Chem. Inf. Model.	2020	DBLP DOI BibTeX RDF
28	Wei Jiang, Christophe Chipot, Benoît Roux	Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD.	J. Chem. Inf. Model.	2019	DBLP DOI BibTeX RDF
28	Junshi Chen, Hong An, Binghui Yan, Weihao Liang, Xin Liu 0081	Redesign NAMD Molecular Dynamics Non-Bonded Force-Field on Sunway Manycore Processor.	HPCC/SmartCity/DSS	2019	DBLP DOI BibTeX RDF
28	Bilge Acun, David J. Hardy, Laxmikant V. Kalé, Keqin Li 0001, James C. Phillips, John E. Stone	Scalable molecular dynamics with NAMD on the Summit system.	IBM J. Res. Dev.	2018	DBLP DOI BibTeX RDF
28	James C. Phillips	What You Should Know About NAMD and Charm++ But Were Hoping to Ignore.	PEARC	2018	DBLP DOI BibTeX RDF
28	John E. Stone, Antti-Pekka Hynninen, James C. Phillips, Klaus Schulten	Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms.	ISC Workshops	2016	DBLP DOI BibTeX RDF
28	Yamandú González, Pablo Ezzatti, Margot Paulino	Unleashing the Graphic Processing Units-Based Version of NAMD.	IWBBIO	2016	DBLP DOI BibTeX RDF
28	Aaron H. Brown, Tiffany R. Walsh	An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture.	Comput. Phys. Commun.	2015	DBLP DOI BibTeX RDF
28	Sunhwan Jo, Wei Jiang	A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations.	Comput. Phys. Commun.	2015	DBLP DOI BibTeX RDF
28	Drasko Tomic	Exploring bacterial biofilms with NAMD, a highly scalable parallel code for complex molecular simulations.	MIPRO	2015	DBLP DOI BibTeX RDF
28	Wei Jiang, James C. Phillips, Lei Huang 0019, Mikolai Fajer, Yilin Meng, James C. Gumbart, Yun Luo, Klaus Schulten, Benoît Roux	Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD.	Comput. Phys. Commun.	2014	DBLP DOI BibTeX RDF
28	James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, Klaus Schulten	Petascale Tcl with NAMD, VMD, and Swift/T.	HPTCDL@SC	2014	DBLP DOI BibTeX RDF
28	James C. Phillips, Klaus Schulten, Abhinav Bhatele, Chao Mei, Yanhua Sun, Eric J. Bohm, Laxmikant V. Kalé	Scalable Molecular Dynamics with NAMD.	Parallel Science and Engineering Applications	2013	DBLP BibTeX RDF
28	Adam K. L. Wong, Andrzej M. Goscinski	A VMD Plugin for NAMD Simulations on Amazon EC2.	ICCS	2012	DBLP DOI BibTeX RDF
28	Armen H. Poghosyan, Levon H. Arsenyan, Hrachya V. Astsatryan	Comparative NAMD benchmarking on BlueGene/P.	MIPRO	2012	DBLP BibTeX RDF
28		NAnoscale Molecular Dynamics (NAMD).	Encyclopedia of Parallel Computing	2011	DBLP DOI BibTeX RDF
28	Laxmikant V. Kalé, Abhinav Bhatele, Eric J. Bohm, James C. Phillips	NAMD (NAnoscale Molecular Dynamics).	Encyclopedia of Parallel Computing	2011	DBLP DOI BibTeX RDF
28	Zhongwei Li, Ebrahim Khosravi, Shuju Bai	Interaction simulation of Lipoxygenase with arachidonate acid using NAMD.	BIBM Workshops	2011	DBLP DOI BibTeX RDF
28	William J. Menz, Matthew J. Penna, Mark J. Biggs	TNAMD: Implementation of TIGER2 in NAMD.	Comput. Phys. Commun.	2010	DBLP DOI BibTeX RDF
28	Sameer Kumar 0001, Chao Huang 0029, Gengbin Zheng, Eric J. Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, Laxmikant V. Kalé	Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system.	IBM J. Res. Dev.	2008	DBLP DOI BibTeX RDF
28	A. B. Mutiara 0001	Analisis Kinerja Sistem Cluster Terhadapa Aplikasi Simulasi Dinamika Molekular NAMD Memanfaatkan Pustaka CHARM++	CoRR	2008	DBLP BibTeX RDF
28	James C. Phillips, Rosemary Braun, Wei Wang 0342, James C. Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant V. Kalé, Klaus Schulten	Scalable molecular dynamics with NAMD.	J. Comput. Chem.	2005	DBLP DOI BibTeX RDF
28	Laxmikant V. Kalé, Milind A. Bhandarkar, Robert Brunner, Neal Krawetz, James C. Phillips, Aritomo Shinozaki	NAMD: A Case Study in Multilingual Parallel Programming.	LCPC	1997	DBLP DOI BibTeX RDF
28	Mark T. Nelson, William Humphrey, Attila Gürsoy, Andrew Dalke, Laxmikant V. Kalé, Robert D. Skeel, Klaus Schulten	NAMD: a Parallel, Object-Oriented Molecular Dynamics Program.	Int. J. High Perform. Comput. Appl.	1996	DBLP DOI BibTeX RDF
19	Allen D. Malony, Scott Biersdorff, Wyatt Spear, Shangkar Mayanglambam	An experimental approach to performance measurement of heterogeneous parallel applications using CUDA.	ICS	2010	DBLP DOI BibTeX RDF	profiling, GPGPU, tracing, performance tools
19	Abhinav Bhatele, Laxmikant V. Kalé, Sameer Kumar 0001	Dynamic topology aware load balancing algorithms for molecular dynamics applications.	ICS	2009	DBLP DOI BibTeX RDF	load balancing, mapping, topology, mesh, torus
19	Ayose Falcón, Paolo Faraboschi, Daniel Ortega	An Adaptive Synchronization Technique for Parallel Simulation of Networked Clusters.	ISPASS	2008	DBLP DOI BibTeX RDF
19	Chee Wai Lee, Celso L. Mendes, Laxmikant V. Kalé	Towards scalable performance analysis and visualization through data reduction.	IPDPS	2008	DBLP DOI BibTeX RDF
19	Sadaf R. Alam, Pratul K. Agarwal, Scott S. Hampton, Hong Ong, Jeffrey S. Vetter	Impact of multicores on large-scale molecular dynamics simulations.	IPDPS	2008	DBLP DOI BibTeX RDF
19	Matthew J. Koop, Terry R. Jones, Dhabaleswar K. Panda 0001	MVAPICH-Aptus: Scalable high-performance multi-transport MPI over InfiniBand.	IPDPS	2008	DBLP DOI BibTeX RDF
19	Abhinav Bhatele, Laxmikant V. Kalé	Application-specific topology-aware mapping for three dimensional topologies.	IPDPS	2008	DBLP DOI BibTeX RDF
19	Matthew J. Koop, Rahul Kumar, Dhabaleswar K. Panda 0001	Can software reliability outperform hardware reliability on high performance interconnects?: a case study with MPI over infiniband.	ICS	2008	DBLP DOI BibTeX RDF	reliability, MPI, infiniband
19	Maciej Malawski, Tomasz Bartynski, Marian Bubak	A Tool for Building Collaborative Applications by Invocation of Grid Operations.	ICCS (3)	2008	DBLP DOI BibTeX RDF	application building, DEISA, Grid computing, tools, virtual laboratory, EGEE
19	James C. Phillips, John E. Stone, Klaus Schulten	Adapting a message-driven parallel application to GPU-accelerated clusters.	SC	2008	DBLP DOI BibTeX RDF
19	Matthew J. Koop, Jaidev K. Sridhar, Dhabaleswar K. Panda 0001	Scalable MPI design over InfiniBand using eXtended Reliable Connection.	CLUSTER	2008	DBLP DOI BibTeX RDF
19	Lei Chai, Qi Gao 0004, Dhabaleswar K. Panda 0001	Understanding the Impact of Multi-Core Architecture in Cluster Computing: A Case Study with Intel Dual-Core System.	CCGRID	2007	DBLP DOI BibTeX RDF
19	David M. Kunzman, Gengbin Zheng, Eric J. Bohm, James C. Phillips, Laxmikant V. Kalé	Poster reception - Charm++ simplifies coding for the cell processor.	SC	2006	DBLP DOI BibTeX RDF
19	Sayantan Sur, Matthew J. Koop, Dhabaleswar K. Panda 0001	MPI and communication - High-performance and scalable MPI over InfiniBand with reduced memory usage: an in-depth performance analysis.	SC	2006	DBLP DOI BibTeX RDF
19	Valentina Salapura, Randy Bickford, Matthias A. Blumrich, Arthur A. Bright, Dong Chen 0005, Paul Coteus, Alan Gara, Mark Giampapa, Michael Gschwind, Manish Gupta 0002, Shawn Hall, Ruud A. Haring, Philip Heidelberger, Dirk Hoenicke, Gerard V. Kopcsay, Martin Ohmacht, Rick A. Rand, Todd Takken, Pavlos Vranas	Power and performance optimization at the system level.	Conf. Computing Frontiers	2005	DBLP DOI BibTeX RDF	BlueGene/L, application performance analysis, application scaling in multiprocessor systems, power/performance efficient systems, power/performance tradeos in systems, chip multiprocessors, supercomputers
19	Sameer Kumar 0001, Laxmikant V. Kalé	Opportunities and Challenges of Modern Communication Architectures: Case Study with QsNet.	IPDPS	2004	DBLP DOI BibTeX RDF
19	Naohito Sato, Jean-Marc Jézéquel	Implementing and Evaluating an Efficient Dynamic Load-Balancer for Distributed Molecular Dynamics Simulation.	ICPP Workshops	2000	DBLP DOI BibTeX RDF