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.

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  1. Acun, Bilge; Buch, Ronak; Kale, Laxmikant; Phillips, James C.: NAMD: scalable molecular dynamics based on the charm++ parallel runtime system (2018)
  2. Ambrosia, Matthew Stanley; Ha, Man Yeong: A molecular dynamics study of wenzel state water droplets on anisotropic surfaces (2018)
  3. Mehrafrooz, Behzad; Shamloo, Amir: Mechanical differences between ATP and ADP actin states: a molecular dynamics study (2018)
  4. Melnick, Corey; Kaviany, Massoud: Thermal actuation in TRPV1: role of embedded lipids and intracellular domains (2018)
  5. Delle Site, Luigi; Praprotnik, Matej: Molecular systems with open boundaries: theory and simulation (2017)
  6. 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)
  7. Bock, Nicolas; Challacombe, Matt; Kalé, Laxmikant V.: Solvers for $\mathcalO(N)$ electronic structure in the strong scaling limit (2016)
  8. 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)
  9. Gogolinska, Anna; Jakubowski, Rafal; Nowak, Wieslaw: Petri nets formalism facilitates analysis of complex biomolecular structural data (2016)
  10. Sun, Kwang Woong; Ambrosia, Matthew Stanley; Kwon, Tae Woo; Ha, Man Yeong: A hydrophobicity study on wavy and orthogonal textured surfaces (2016)
  11. 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)
  12. Trȩdak, Przemysław; Rudnicki, Witold R.; Majewski, Jacek A.: Efficient implementation of the many-body reactive bond order (REBO) potential on GPU (2016)
  13. 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)
  14. Zhang, Peng; Zhang, Na; Deng, Yuefan; Bluestein, Danny: A multiple time stepping algorithm for efficient multiscale modeling of platelets flowing in blood plasma (2015)
  15. 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
  16. 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)
  17. Krause, Dorian; Fackeldey, Konstantin; Krause, Rolf: A parallel multiscale simulation toolbox for coupling molecular dynamics and finite elements (2014)
  18. 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
  19. Xie, Dexuan: New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics (2014)
  20. 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)

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