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181 related items for PubMed ID: 26589055

  • 1. Replica-Permutation Method with the Suwa-Todo Algorithm beyond the Replica-Exchange Method.
    Itoh SG, Okumura H.
    J Chem Theory Comput; 2013 Jan 08; 9(1):570-81. PubMed ID: 26589055
    [Abstract] [Full Text] [Related]

  • 2. Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides.
    Itoh SG, Okumura H.
    J Comput Chem; 2013 Nov 05; 34(29):2493-7. PubMed ID: 23925979
    [Abstract] [Full Text] [Related]

  • 3. Development of isothermal-isobaric replica-permutation method for molecular dynamics and Monte Carlo simulations and its application to reveal temperature and pressure dependence of folded, misfolded, and unfolded states of chignolin.
    Yamauchi M, Okumura H.
    J Chem Phys; 2017 Nov 14; 147(18):184107. PubMed ID: 29141431
    [Abstract] [Full Text] [Related]

  • 4. Replica state exchange metadynamics for improving the convergence of free energy estimates.
    Galvelis R, Sugita Y.
    J Comput Chem; 2015 Jul 15; 36(19):1446-55. PubMed ID: 25990969
    [Abstract] [Full Text] [Related]

  • 5. Replica sub-permutation method for molecular dynamics and monte carlo simulations.
    Yamauchi M, Okumura H.
    J Comput Chem; 2019 Dec 05; 40(31):2694-2711. PubMed ID: 31365132
    [Abstract] [Full Text] [Related]

  • 6. Coulomb replica-exchange method: handling electrostatic attractive and repulsive forces for biomolecules.
    Itoh SG, Okumura H.
    J Comput Chem; 2013 Mar 30; 34(8):622-39. PubMed ID: 23197415
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  • 9. Transformation of a design peptide between the α-helix and β-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation.
    Okumura H, Itoh SG.
    Phys Chem Chem Phys; 2013 Sep 07; 15(33):13852-61. PubMed ID: 23839056
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  • 10. Enhanced exchange algorithm without detailed balance condition for replica exchange method.
    Kondo HX, Taiji M.
    J Chem Phys; 2013 Jun 28; 138(24):244113. PubMed ID: 23822233
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  • 11. Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm.
    Zhou R.
    J Mol Graph Model; 2004 May 28; 22(5):451-63. PubMed ID: 15099840
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  • 12. Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency.
    Fukuhara D, Yamauchi M, Itoh SG, Okumura H.
    J Comput Chem; 2023 Feb 05; 44(4):534-545. PubMed ID: 36346137
    [Abstract] [Full Text] [Related]

  • 13. Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method.
    Chaudhury S, Olson MA, Tawa G, Wallqvist A, Lee MS.
    J Chem Theory Comput; 2012 Feb 14; 8(2):677-87. PubMed ID: 26596615
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  • 14. 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
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  • 15. Replica exchange molecular dynamics method for protein folding simulation.
    Zhou R.
    Methods Mol Biol; 2007 May 14; 350():205-23. PubMed ID: 16957325
    [Abstract] [Full Text] [Related]

  • 16. MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.
    Yamamori Y, Kitao A.
    J Chem Phys; 2013 Oct 14; 139(14):145105. PubMed ID: 24116651
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  • 18. Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations.
    Yoda T, Sugita Y, Okamoto Y.
    Proteins; 2014 Jun 14; 82(6):933-43. PubMed ID: 24214490
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