AMBER

AmberTools is a set of programs for biomolecular simulation and analysis. They are designedto work well with each other, and with the “regular” Amber suite of programs. You can performmany simulation tasks with AmberTools, and you can do more extensive simulations with thecombination of AmberTools and Amber itself.


References in zbMATH (referenced in 36 articles , 1 standard article )

Showing results 1 to 20 of 36.
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  1. Kulik, Marta; Trylska, Joanna: Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site (2016)
  2. Leimkuhler, Benedict; Shang, Xiaocheng: Adaptive thermostats for noisy gradient systems (2016)
  3. Trȩdak, Przemysław; Rudnicki, Witold R.; Majewski, Jacek A.: Efficient implementation of the many-body reactive bond order (REBO) potential on GPU (2016)
  4. Nicholas P. Bailey, Trond S. Ingebrigtsen, Jesper Schmidt Hansen, Arno A. Veldhorst, Lasse Bohling, Claire A. Lemarchand, Andreas E. Olsen, Andreas K. Bacher, Lorenzo Costigliola, Ulf R. Pedersen, Heine Larsen, Jeppe C. Dyre, Thomas B. Schroder: RUMD: A general purpose molecular dynamics package optimized to utilize GPU hardware down to a few thousand particles (2015) arXiv
  5. Yang, Edward Z.; Campagna, Giovanni; Ağacan, Ömer S.; El-Hassany, Ahmed; Kulkarni, Abhishek; Newton, Ryan R.: Efficient communication and collection with compact normal forms (2015)
  6. 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
  7. Poursina, Mohammad; Anderson, Kurt S.: An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations (2014)
  8. Anderson, Joshua A.; Jankowski, Eric; Grubb, Thomas L.; Engel, Michael; Glotzer, Sharon C.: Massively parallel Monte Carlo for many-particle simulations on GPUs (2013)
  9. Geng, Weihua; Jacob, Ferosh: A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver (2013)
  10. Oden, J.Tinsley; Prudencio, Ernesto E.; Bauman, Paul T.: Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics (2013)
  11. Geng, Weihua; Wei, G.W.: Multiscale molecular dynamics using the matched interface and boundary method (2011)
  12. Lindbo, Dag; Tornberg, Anna-Karin: Spectral accuracy in fast Ewald-based methods for particle simulations (2011)
  13. M. N. Bannerman, R. Sargant, L. Lue: DynamO: A free O(N) general event-driven molecular-dynamics simulator (2010) arXiv
  14. Weggler, S.; Rutka, V.; Hildebrandt, A.: A new numerical method for nonlocal electrostatics in biomolecular simulations (2010)
  15. Greenstein, Gil; Ahituv, Niv: The value of knowing that you do not know (2009)
  16. Håkan, Hugosson W.; Ågren, Hans: Quantum mechanics/Classical mechanics modeling of biological systems (2009)
  17. M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R. A. Broglia, M. Parrinello: PLUMED: a portable plugin for free-energy calculations with molecular dynamics (2009) arXiv
  18. Tarasov, D.S.; Izotova, E.D.; Alisheva, D.A.; Akberova, N.I.: GPAMM-software package for molecular dynamics on graphical processing units (2009)
  19. Haberl, Florian; Othersen, Olaf; Seidel, Ute; Lanig, Harald; Clark, Tim: Investigating protein-protein and protein-ligand interactions by molecular dynamics simulations (2008)
  20. Mukherjee, Rudranarayan M.; Crozier, Paul S.; Plimpton, Steven J.; Anderson, Kurt S.: Substructured molecular dynamics using multibody dynamics algorithms (2008)

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