NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms.

References in zbMATH (referenced in 79 articles )

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  1. Salas, Gicela G. Saucedo; Hernandez, Alan E. Lopez; He, Jiadi; Karki, Chitra; Xie, Yixin; Sun, Shengjie; Xian, Yuejiao; Li, Lin: Using computational approaches to study dengue virus capsid assembly (2019)
  2. Younes Nejahi; Mohammad Soroush Barhaghi; Jason Mick; Brock Jackman; Kamel Rushaidat; Yuanzhe Li; Loren Schwiebert; Jeffrey Potoff: GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids (2019) not zbMATH
  3. Acun, Bilge; Buch, Ronak; Kale, Laxmikant; Phillips, James C.: NAMD: scalable molecular dynamics based on the charm++ parallel runtime system (2018)
  4. Ambrosia, Matthew Stanley; Ha, Man Yeong: A molecular dynamics study of wenzel state water droplets on anisotropic surfaces (2018)
  5. Fu, Yi; Zhao, Ji; Chen, Zhiguo; Chen, Xiaole: Insights into the molecular mechanisms of protein-ligand interactions by molecular docking and molecular dynamics simulation: a case of oligopeptide binding protein (2018)
  6. Horacio V. Guzman, Nikita Tretyakov, Hideki Kobayashi, Aoife C. Fogarty, Karsten Kreis, Jakub Krajniak, Christoph Junghans, Kurt Kremer, Torsten Stuehn: ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation (2018) arXiv
  7. Jiang, Xi Zhuo; Feng, Muye; Luo, Kai H.; Ventikos, Yiannis: Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx (2018)
  8. Polyakov, S. V.; Podryga, V. O.; Puzyrkov, D. V.: High performance computing in multiscale problems of gas dynamics (2018)
  9. Delle Site, Luigi; Praprotnik, Matej: Molecular systems with open boundaries: theory and simulation (2017)
  10. Kidder, Lawrence E.; Field, Scott E.; Foucart, Francois; Schnetter, Erik; Teukolsky, Saul A.; Bohn, Andy; Deppe, Nils; Diener, Peter; Hébert, François; Lippuner, Jonas; Miller, Jonah; Ott, Christian D.; Scheel, Mark A.; Vincent, Trevor: SpECTRE: A task-based discontinuous Galerkin code for relativistic astrophysics (2017)
  11. Bock, Nicolas; Challacombe, Matt; Kalé, Laxmikant V.: Solvers for (\mathcalO(N)) electronic structure in the strong scaling limit (2016)
  12. Gebbie-Rayet, J., Shannon, G., Loeffler, H.H., Laughton, C.A.: Longbow: A Lightweight Remote Job Submission Tool (2016) not zbMATH
  13. Gholami, Amir; Malhotra, Dhairya; Sundar, Hari; Biros, George: FFT, FMM, or multigrid? A comparative study of state-of-the-art Poisson solvers for uniform and nonuniform grids in the unit cube (2016)
  14. Gogolinska, Anna; Jakubowski, Rafal; Nowak, Wieslaw: Petri nets formalism facilitates analysis of complex biomolecular structural data (2016)
  15. Sun, Kwang Woong; Ambrosia, Matthew Stanley; Kwon, Tae Woo; Ha, Man Yeong: A hydrophobicity study on wavy and orthogonal textured surfaces (2016)
  16. Tardu, Mehmet; Rahim, Fatih; Kavakli, I. Halil; Turkay, Metin: Milp-hyperbox classification for structure-based drug design in the discovery of small molecule inhibitors of SIRTUIN6 (2016)
  17. Trȩdak, Przemysław; Rudnicki, Witold R.; Majewski, Jacek A.: Efficient implementation of the many-body reactive bond order (REBO) potential on GPU (2016)
  18. Ko, Jeong-Ahn; Ambrosia, Matthew; Ha, Man Yeong: A study of the wetting characteristics of a nano-sized water droplet on heterogeneous striped surfaces (2015)
  19. Mark James Abraham; Teemu Murtola; Roland Schulz; Szilárd Páll; Jeremy C.Smith; Berk Hess; Erik Lindahl: GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers (2015) not zbMATH
  20. Zhang, Peng; Zhang, Na; Deng, Yuefan; Bluestein, Danny: A multiple time stepping algorithm for efficient multiscale modeling of platelets flowing in blood plasma (2015)

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