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Journal Abstract Search

358 related items for PubMed ID: 16323162

  • 1. Monte Carlo simulations of biomolecules: The MC module in CHARMM.
    Hu J, Ma A, Dinner AR.
    J Comput Chem; 2006 Jan 30; 27(2):203-16. PubMed ID: 16323162
    [Abstract] [Full Text] [Related]

  • 2. Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.
    Okumura H.
    J Chem Phys; 2008 Sep 28; 129(12):124116. PubMed ID: 19045015
    [Abstract] [Full Text] [Related]

  • 3. Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.
    van der Vaart A, Karplus M.
    J Chem Phys; 2007 Apr 28; 126(16):164106. PubMed ID: 17477588
    [Abstract] [Full Text] [Related]

  • 4. Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations.
    Okamoto Y.
    J Mol Graph Model; 2004 May 28; 22(5):425-39. PubMed ID: 15099838
    [Abstract] [Full Text] [Related]

  • 5. Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations.
    Ulmschneider JP, Ulmschneider MB, Di Nola A.
    J Phys Chem B; 2006 Aug 24; 110(33):16733-42. PubMed ID: 16913813
    [Abstract] [Full Text] [Related]

  • 6. Multiple "time step" Monte Carlo simulations: application to charged systems with Ewald summation.
    Bernacki K, Hetenyi B, Berne BJ.
    J Chem Phys; 2004 Jul 01; 121(1):44-50. PubMed ID: 15260521
    [Abstract] [Full Text] [Related]

  • 7. Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol.
    Velez-Vega C, Borrero EE, Escobedo FA.
    J Chem Phys; 2009 Jun 14; 130(22):225101. PubMed ID: 19530790
    [Abstract] [Full Text] [Related]

  • 8. Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent.
    Okumura H.
    Phys Chem Chem Phys; 2011 Jan 07; 13(1):114-26. PubMed ID: 21038036
    [Abstract] [Full Text] [Related]

  • 9. On use of the Amber potential with the Langevin dipole method.
    Mijajlovic M, Biggs MJ.
    J Phys Chem B; 2007 Jul 05; 111(26):7591-602. PubMed ID: 17550281
    [Abstract] [Full Text] [Related]

  • 10. Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.
    Cooke B, Schmidler SC.
    J Chem Phys; 2008 Oct 28; 129(16):164112. PubMed ID: 19045252
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  • 11. Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo method: application to peptides.
    Cheluvaraja S, Meirovitch H.
    J Chem Phys; 2005 Feb 01; 122(5):54903. PubMed ID: 15740349
    [Abstract] [Full Text] [Related]

  • 12. An efficient framework for photon Monte Carlo treatment planning.
    Fix MK, Manser P, Frei D, Volken W, Mini R, Born EJ.
    Phys Med Biol; 2007 Oct 07; 52(19):N425-37. PubMed ID: 17881793
    [Abstract] [Full Text] [Related]

  • 13. Unorthodox uses of Bennett's acceptance ratio method.
    König G, Bruckner S, Boresch S.
    J Comput Chem; 2009 Aug 07; 30(11):1712-8. PubMed ID: 19373838
    [Abstract] [Full Text] [Related]

  • 14. Biased fragment distribution in MC simulation of protein folding.
    Martineau E, L'Heureux PJ, Gunn JR.
    J Comput Chem; 2004 Nov 30; 25(15):1895-903. PubMed ID: 15378533
    [Abstract] [Full Text] [Related]

  • 15. An artificial intelligence approach for modeling molecular self-assembly: agent-based simulations of rigid molecules.
    Fortuna S, Troisi A.
    J Phys Chem B; 2009 Jul 23; 113(29):9877-85. PubMed ID: 19569637
    [Abstract] [Full Text] [Related]

  • 16. Generalized-ensemble algorithms for molecular simulations of biopolymers.
    Mitsutake A, Sugita Y, Okamoto Y.
    Biopolymers; 2001 Jul 23; 60(2):96-123. PubMed ID: 11455545
    [Abstract] [Full Text] [Related]

  • 17. Reconstructing atomistic detail for coarse-grained models with resolution exchange.
    Liu P, Shi Q, Lyman E, Voth GA.
    J Chem Phys; 2008 Sep 21; 129(11):114103. PubMed ID: 19044946
    [Abstract] [Full Text] [Related]

  • 18. A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): application to highly solvent-dependent reactions.
    Hori K, Yamaguchi T, Uezu K, Sumimoto M.
    J Comput Chem; 2011 Apr 15; 32(5):778-86. PubMed ID: 21341291
    [Abstract] [Full Text] [Related]

  • 19. Solvent-shift Monte Carlo: a cluster algorithm for solvated systems.
    Hixson CA, Benigni JP, Earl DJ.
    Phys Chem Chem Phys; 2009 Aug 14; 11(30):6335-8. PubMed ID: 19809663
    [Abstract] [Full Text] [Related]

  • 20. LOOPER: a molecular mechanics-based algorithm for protein loop prediction.
    Spassov VZ, Flook PK, Yan L.
    Protein Eng Des Sel; 2008 Feb 14; 21(2):91-100. PubMed ID: 18194981
    [Abstract] [Full Text] [Related]

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