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 23 articles )

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  1. 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)
  2. Wu, Qiang; Yang, Canqun; Tang, Tao; Xiao, Liquan: Exploiting hierarchy parallelism for molecular dynamics on a petascale heterogeneous system (2013)
  3. Lilkova, Elena; Nacheva, Genoveva; Petkov, Peicho; Petkov, Petko; Markov, Stoyan; Ilieva, Nevena; Litov, Leandar: Metadynamics study of mutant human interferon-gamma forms (2012)
  4. Xie, Dexuan; Zarrouk, Mazen G.: Convergence analysis of truncated incomplete Hessian Newton minimization method and application in biomolecular potential energy minimization (2011)
  5. Anitescu, Mihai; Park, Sanghyun: A linear assignment approach for the least-squares protein morphing problem (2010)
  6. Menz, William J.; Penna, Matthew J.; Biggs, Mark J.: TNAMD: Implementation of TIGER2 in NAMD (2010)
  7. Kutnar, Klavdija; Borštnik, Urban; Marušič, Dragan; Janežič, Dušanka: Interconnection networks for parallel molecular dynamics simulation based on Hamiltonian cubic symmetric topology (2009)
  8. Anandampillai, S.; Zhang, X.; Sharma, P.; Lynch, Gillian C.; Franchek, M.A.; Larin, K.V.: Quantum dot-DNA interaction: Computational issues and preliminary insights on use of quantum dots as biosensors (2008)
  9. Keten, Sinan; Buehler, Markus J.: Large deformation and fracture mechanics of a beta-helical protein nanotube: Atomistic and continuum modeling (2008)
  10. Poghosyan, Armen H.; Gharabekyan, Hrant H.; Shahinyan, Aram A.: Molecular dynamics simulations of DMPC/DPPC mixed bilayers (2007)
  11. Poghosyan, A.H.; Yeghiazaryan, G.A.; Gharabekyan, H.H.; Shahinyan, A.A.: The GROMACS and NAMD software packages comparison. (2006)
  12. Wang, Kai; Chang, Anthony; Kale, Laxmikant V.; Dantzig, Jonathan A.: Parallelization of a level set method for simulating dendritic growth (2006)
  13. Ma, Qun; Izaguirre, Jesús A.: Targeted mollified impulse: a multiscale stochastic integrator for long molecular dynamics simulations (2004)
  14. Zimmermann, Karl-Heinz: A special purpose array processor architecture for the molecular dynamics simulation of point-mutated proteins (2003)
  15. Izaguirre, Jesús A.; Ma, Qun; Matthey, Thierry; Willcock, Jeremiah; Slabach, Thomas; Moore, Branden; Viamontes, George: Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method (2002)
  16. Peters, Bernhard; Dẓiugys, Algis: Numerical simulation of the motion of granular material using object-oriented techniques (2002)
  17. Kamberaj, H.; Helms, V.: Monte Carlo simulation of biomolecular systems with BIOMCSIM (2001)
  18. Izrailev, Sergei; Stepaniants, Sergey; Isralewitz, Barry; Kosztin, Dorina; Lu, Hui; Molnar, Ferenc; Wriggers, Willy; Schulten, Klaus: Steered molecular dynamics (1999)
  19. Kalé, Laxmikant; Skeel, Robert; Bhandarkar, Milind; Brunner, Robert; Gursoy, Attila; Krawetz, Neal; Phillips, James; Shinozaki, Aritomo; Varadarajan, Krishnan; Schulten, Klaus: NAMD2: Greater scalability for parallel molecular dynamics (1999)
  20. Phillips, James C.; Brunner, Robert; Shinozaki, Aritomo; Bhandakar, Milind; Kraewetz, Neal; Gursoy, Attila; Kalé, Laxmikant; Skeel, Robert D.; Schulten, Klaus: Avoiding algorithmic obfuscation in a message-driven parallel MD code (1999)

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