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170 related items for PubMed ID: 18052416

  • 1. Optimization of replica exchange molecular dynamics by fast mimicking.
    Hritz J, Oostenbrink C.
    J Chem Phys; 2007 Nov 28; 127(20):204104. PubMed ID: 18052416
    [Abstract] [Full Text] [Related]

  • 2. Hamiltonian replica exchange molecular dynamics using soft-core interactions.
    Hritz J, Oostenbrink C.
    J Chem Phys; 2008 Apr 14; 128(14):144121. PubMed ID: 18412437
    [Abstract] [Full Text] [Related]

  • 3. Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems.
    Vreede J, Wolf MG, de Leeuw SW, Bolhuis PG.
    J Phys Chem B; 2009 May 07; 113(18):6484-94. PubMed ID: 19358572
    [Abstract] [Full Text] [Related]

  • 4. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent.
    Periole X, Mark AE.
    J Chem Phys; 2007 Jan 07; 126(1):014903. PubMed ID: 17212515
    [Abstract] [Full Text] [Related]

  • 5. Convergence of replica exchange molecular dynamics.
    Zhang W, Wu C, Duan Y.
    J Chem Phys; 2005 Oct 15; 123(15):154105. PubMed ID: 16252940
    [Abstract] [Full Text] [Related]

  • 6. Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: assessing entropic and environmental effects.
    Faraldo-Gómez JD, Roux B.
    J Comput Chem; 2007 Jul 30; 28(10):1634-47. PubMed ID: 17342721
    [Abstract] [Full Text] [Related]

  • 7. Replica exchange molecular dynamics simulations of amyloid peptide aggregation.
    Cecchini M, Rao F, Seeber M, Caflisch A.
    J Chem Phys; 2004 Dec 01; 121(21):10748-56. PubMed ID: 15549960
    [Abstract] [Full Text] [Related]

  • 8. Replica exchange simulation method using temperature and solvent viscosity.
    Nguyen PH.
    J Chem Phys; 2010 Apr 14; 132(14):144109. PubMed ID: 20405987
    [Abstract] [Full Text] [Related]

  • 9. Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space.
    Chen C, Xiao Y, Huang Y.
    Phys Rev E Stat Nonlin Soft Matter Phys; 2015 May 14; 91(5):052708. PubMed ID: 26066200
    [Abstract] [Full Text] [Related]

  • 10. Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers.
    Hritz J, Oostenbrink C.
    J Phys Chem B; 2009 Sep 24; 113(38):12711-20. PubMed ID: 19722597
    [Abstract] [Full Text] [Related]

  • 11. Exchange frequency in replica exchange molecular dynamics.
    Sindhikara D, Meng Y, Roitberg AE.
    J Chem Phys; 2008 Jan 14; 128(2):024103. PubMed ID: 18205439
    [Abstract] [Full Text] [Related]

  • 12. An improved replica-exchange sampling method: temperature intervals with global energy reassignment.
    Li X, O'Brien CP, Collier G, Vellore NA, Wang F, Latour RA, Bruce DA, Stuart SJ.
    J Chem Phys; 2007 Oct 28; 127(16):164116. PubMed ID: 17979328
    [Abstract] [Full Text] [Related]

  • 13. Optimized explicit-solvent replica exchange molecular dynamics from scratch.
    Nadler W, Hansmann UH.
    J Phys Chem B; 2008 Aug 28; 112(34):10386-7. PubMed ID: 18671362
    [Abstract] [Full Text] [Related]

  • 14. ETNA: equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations.
    Muff S, Caflisch A.
    J Phys Chem B; 2009 Mar 12; 113(10):3218-26. PubMed ID: 19231819
    [Abstract] [Full Text] [Related]

  • 15. Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling method.
    Kannan S, Zacharias M.
    J Struct Biol; 2009 Jun 12; 166(3):288-94. PubMed ID: 19272454
    [Abstract] [Full Text] [Related]

  • 16. Reversible folding simulation by hybrid Hamiltonian replica exchange.
    Xu W, Lai T, Yang Y, Mu Y.
    J Chem Phys; 2008 May 07; 128(17):175105. PubMed ID: 18465944
    [Abstract] [Full Text] [Related]

  • 17. Conformational space search of Neuromedin C using replica exchange molecular dynamics and molecular dynamics.
    Sharma P, Singh P, Bisetty K, Rodriguez A, Perez JJ.
    J Pept Sci; 2011 Mar 07; 17(3):174-83. PubMed ID: 20878681
    [Abstract] [Full Text] [Related]

  • 18. Demixing transition of the aqueous solution of amyloidogenic peptides: a REMD simulation study.
    Singh G, Brovchenko I, Oleinikova A, Winter R.
    J Phys Chem B; 2009 Jul 23; 113(29):9863-70. PubMed ID: 19569617
    [Abstract] [Full Text] [Related]

  • 19. How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach.
    Nymeyer H.
    J Chem Theory Comput; 2008 Apr 23; 4(4):626-36. PubMed ID: 26620937
    [Abstract] [Full Text] [Related]

  • 20. Replica exchange with dynamical scaling.
    Rick SW.
    J Chem Phys; 2007 Feb 07; 126(5):054102. PubMed ID: 17302469
    [Abstract] [Full Text] [Related]

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