NAMD

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 54 articles )

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  1. Bock, Nicolas; Challacombe, Matt; Kalé, Laxmikant V.: Solvers for $\mathcalO(N)$ electronic structure in the strong scaling limit (2016)
  2. 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)
  3. Gogolinska, Anna; Jakubowski, Rafal; Nowak, Wieslaw: Petri nets formalism facilitates analysis of complex biomolecular structural data (2016)
  4. 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)
  5. Trȩdak, Przemysław; Rudnicki, Witold R.; Majewski, Jacek A.: Efficient implementation of the many-body reactive bond order (REBO) potential on GPU (2016)
  6. Zhang, Peng; Zhang, Na; Deng, Yuefan; Bluestein, Danny: A multiple time stepping algorithm for efficient multiscale modeling of platelets flowing in blood plasma (2015)
  7. Ding, Jin-Hong; Li, Ning; Wang, Man-Liu; Zhang, Yan; Lü, Shou-Qin; Long, Mian: The impact of N-terminal phosphorylation on LHCII conformation in state transition (2014) ioport
  8. Kojic, M.; Milosevic, M.; Kojic, N.; Kim, K.; Ferrari, M.; Ziemys, A.: A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure (2014)
  9. Pal, Anirban; Agarwala, Abhishek; Raha, Soumyendu; Bhattacharya, Baidurya: Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions (2014) ioport
  10. Xie, Dexuan: New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics (2014)
  11. Arnold, Axel; Lenz, Olaf; Kesselheim, Stefan; Weeber, Rudolf; Fahrenberger, Florian; Roehm, Dominic; Košovan, Peter; Holm, Christian: ESPResSO 3.1: molecular dynamics software for coarse-grained models (2013)
  12. Wu, Qiang; Yang, Canqun; Tang, Tao; Xiao, Liquan: Exploiting hierarchy parallelism for molecular dynamics on a petascale heterogeneous system (2013) ioport
  13. Yakubovich, Alexander V.; Solov’yov, Andrey V.; Greiner, Walter: Statistical mechanical theory of protein folding in water environment (2013)
  14. Aktulga, H.M.; Fogarty, J.C.; Pandit, S.A.; Grama, A.Y.: Parallel reactive molecular dynamics: numerical methods and algorithmic techniques (2012) ioport
  15. Fackeldey, Konstantin; Klimm, Martina; Weber, Marcus: A coarse graining method for the dimension reduction of the state space of biomolecules (2012)
  16. Gonnet, Pedro: A short note on the fast evaluation of dihedral angle potentials and their derivatives (2012)
  17. Lilkova, Elena; Nacheva, Genoveva; Petkov, Peicho; Petkov, Petko; Markov, Stoyan; Ilieva, Nevena; Litov, Leandar: Metadynamics study of mutant human interferon-gamma forms (2012)
  18. Lindbo, Dag; Tornberg, Anna-Karin: Spectral accuracy in fast Ewald-based methods for particle simulations (2011)
  19. Tsoulos, Ioannis G.; Stavrakoudis, Athanassios: Eucb: a C++ program for molecular dynamics trajectory analysis (2011)
  20. Vaitheeswaran, S.; Chen, Jie; Thirumalai, D.: Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins (2011)

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Further publications can be found at: http://www.ks.uiuc.edu/Publications/Papers/