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Journal Abstract Search

199 related items for PubMed ID: 30183291

  • 1. Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water.
    Sun D, Lakkaraju SK, Jo S, MacKerell AD.
    J Chem Theory Comput; 2018 Oct 09; 14(10):5290-5302. PubMed ID: 30183291
    [Abstract] [Full Text] [Related]

  • 2. Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations.
    Lakkaraju SK, Raman EP, Yu W, MacKerell AD.
    J Chem Theory Comput; 2014 Jun 10; 10(6):2281-2290. PubMed ID: 24932136
    [Abstract] [Full Text] [Related]

  • 3. Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo.
    Ge Y, Melling OJ, Dong W, Essex JW, Mobley DL.
    J Comput Aided Mol Des; 2022 Oct 10; 36(10):767-779. PubMed ID: 36198874
    [Abstract] [Full Text] [Related]

  • 4. Grand canonical Monte Carlo simulations of water in protein environments.
    Woo HJ, Dinner AR, Roux B.
    J Chem Phys; 2004 Oct 01; 121(13):6392-400. PubMed ID: 15446937
    [Abstract] [Full Text] [Related]

  • 5. GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations.
    Zhao M, Kognole AA, Jo S, Tao A, Hazel A, MacKerell AD.
    J Comput Chem; 2023 Jul 30; 44(20):1719-1732. PubMed ID: 37093676
    [Abstract] [Full Text] [Related]

  • 6. Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study.
    Korolev N, Lyubartsev AP, Nordenskiöld L, Laaksonen A.
    J Mol Biol; 2001 May 18; 308(5):907-17. PubMed ID: 11352581
    [Abstract] [Full Text] [Related]

  • 7. Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo.
    Ross GA, Bruce Macdonald HE, Cave-Ayland C, Cabedo Martinez AI, Essex JW.
    J Chem Theory Comput; 2017 Dec 12; 13(12):6373-6381. PubMed ID: 29091438
    [Abstract] [Full Text] [Related]

  • 8. Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo.
    Melling OJ, Samways ML, Ge Y, Mobley DL, Essex JW.
    J Chem Theory Comput; 2023 Feb 14; 19(3):1050-1062. PubMed ID: 36692215
    [Abstract] [Full Text] [Related]

  • 9. Thermodynamics and partitioning of homopolymers into a slit-A grand canonical Monte Carlo simulation study.
    Jiang W, Wang Y.
    J Chem Phys; 2004 Aug 22; 121(8):3905-13. PubMed ID: 15303959
    [Abstract] [Full Text] [Related]

  • 10. Modeling the Nucleation of Weak Electrolytes via Hybrid GCMC/MD Simulation.
    Li X, Schmidt JR.
    J Chem Theory Comput; 2019 Nov 12; 15(11):5883-5893. PubMed ID: 31588744
    [Abstract] [Full Text] [Related]

  • 11. Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks.
    Ekberg V, Samways ML, Misini Ignjatović M, Essex JW, Ryde U.
    ACS Phys Chem Au; 2022 May 25; 2(3):247-259. PubMed ID: 35637786
    [Abstract] [Full Text] [Related]

  • 12. Reactive Grand-Canonical Monte Carlo Simulations for Modeling Hydration of MgCl2.
    Heijmans K, Tranca IC, Chang MW, Vlugt TJH, Gaastra-Nedea SV, Smeulders DMJ.
    ACS Omega; 2021 Dec 07; 6(48):32475-32484. PubMed ID: 34901597
    [Abstract] [Full Text] [Related]

  • 13. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations.
    Deng Y, Roux B.
    J Chem Phys; 2008 Mar 21; 128(11):115103. PubMed ID: 18361618
    [Abstract] [Full Text] [Related]

  • 14. Molecular simulations of confined liquids: an alternative to the grand canonical Monte Carlo simulations.
    Ghoufi A, Morineau D, Lefort R, Hureau I, Hennous L, Zhu H, Szymczyk A, Malfreyt P, Maurin G.
    J Chem Phys; 2011 Feb 21; 134(7):074104. PubMed ID: 21341825
    [Abstract] [Full Text] [Related]

  • 15. py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD.
    Barhaghi MS, Crawford B, Schwing G, Hardy DJ, Stone JE, Schwiebert L, Potoff J, Tajkhorshid E.
    J Chem Theory Comput; 2022 Aug 09; 18(8):4983-4994. PubMed ID: 35621307
    [Abstract] [Full Text] [Related]

  • 16. A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels.
    Im W, Seefeld S, Roux B.
    Biophys J; 2000 Aug 09; 79(2):788-801. PubMed ID: 10920012
    [Abstract] [Full Text] [Related]

  • 17. Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations.
    Yoon H, Kolev V, Warshel A.
    J Phys Chem B; 2017 Oct 12; 121(40):9358-9365. PubMed ID: 28911225
    [Abstract] [Full Text] [Related]

  • 18. Reactive Monte Carlo and grand-canonical Monte Carlo simulations of the propene metathesis reaction system.
    Hansen N, Jakobtorweihen S, Keil FJ.
    J Chem Phys; 2005 Apr 22; 122(16):164705. PubMed ID: 15945697
    [Abstract] [Full Text] [Related]

  • 19. Enabling grand-canonical Monte Carlo: extending the flexibility of GROMACS through the GromPy python interface module.
    Pool R, Heringa J, Hoefling M, Schulz R, Smith JC, Feenstra KA.
    J Comput Chem; 2012 May 05; 33(12):1207-14. PubMed ID: 22370965
    [Abstract] [Full Text] [Related]

  • 20. An efficient iterative grand canonical Monte Carlo algorithm to determine individual ionic chemical potentials in electrolytes.
    Malasics A, Boda D.
    J Chem Phys; 2010 Jun 28; 132(24):244103. PubMed ID: 20590177
    [Abstract] [Full Text] [Related]

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