In Proceedings of the 2012 ACM/IEEE Conference on Supercomputing (SC12), 2012.ĭavid E. Optimizing Fine-grained Communication in a Biomolecular Simulation Application on Cray XK6. Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD.Ĭomputer Physics Communications, 185:908-916, 2014. Wei Jiang, James Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James Gumbart, Yun Luo, Klaus Schulten, and Benoit Roux. In SC'14 workshop on High Performance Technical Computing in Dynamic Languages, SC '14. Petascale Tcl with NAMD, VMD, and Swift/T. Wozniak, Michael Wilde, and Klaus Schulten. In Proceedings of the 2014 International Conference for High Performance Computing, Networking, Storage, and Analysis (SC14), 2014. Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Multiple-replica strategies for free-energy calculations in NAMD: Multiple-walker adaptive biasing force and walker selection rules. Jeffrey Comer, James Phillips, Klaus Schulten, and Christophe Chipot. Journal of Chemical Theory and Computation, 2014. Multilevel Summation Method for Electrostatic Force Evaluation. International Workshop on OpenPOWER for HPC (IWOPH'16), 2016. Phillips, and Klaus Schulten.Įarly experiences porting the NAMD and VMD molecular simulation and analysis software to GPU-accelerated OpenPOWER platforms. QwikMD-integrative molecular dynamics toolkit for novices and experts. Phillips, Klaus Schulten, and Benoît Roux.Ĭonstant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. Radak, Christophe Chipot, Donghyuk Suh, Sunhwan Jo, Wei Jiang, James C. NAMD: Scalable Molecular Dynamics Based on the Charm++ Parallel Runtime System.Įxascale Scientific Applications: Scalability and Performance Portability, Nature Methods, volume 15, pages 351-354, 2018.īilge Acun, Ronak Buch, Laxmikant Kale, and James C. NAMD goes quantum: an integrative suite for hybrid simulations. Marcelo C R Melo, Rafael C Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James C Phillips, Julio D C Maia, Gerd B Rocha, João V Ribeiro, John E Stone, Frank Neese, Klaus Schulten, & Zaida Luthey-Schulten. ACM, New York, NY, USA, Article 55, 6 pages. In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18).
What You Should Know About NAMD and Charm++ But Were Hoping to Ignore. IBM Journal of Research and Development, 2018. Scalable Molecular Dynamics with NAMD on the Summit System. Thank you for your attention to these details.ī. Proper citation is essential to continued NIH funding for NAMD development,Īs it is a primary way in which we demonstrate the value of our software
doi:10.1063/5.0014475Įlectronic documents shall include a direct link to the official Scalable molecular dynamics on CPU and GPU architectures with NAMD. Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid. Skeel, Abhishek Singharoy, Yi Wang, Benoit Roux,Īleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Jerome Henin, Wei Jiang, Ryan McGreevy, Marcelo C. University of Illinois at Urbana-Champaign."Īny published work which utilizes NAMD shall include the following In the Beckman Institute for Advanced Science and Technology at the "NAMD was developed by the Theoretical and Computational Biophysics Group Results obtained with NAMD shall acknowledge its use and credit the The NAMD License Agreement specifies that any reports or published A list of papers citing NAMD is included below.
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