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Molecular Simulation Volume 30, 2004 - Issue 1
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Original Articles

ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules

Andreas Vitalis* Department of Chemistry and Biochemistry, University of California at San Diego, Gilman Dr., Mail Code, 92093-0365, San Diego, CA, USA
,
Nathan A. Baker Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University School of Medicine, 700 S. Euclid Avenue, 63110, St. Louis, MO, USACorrespondence[email protected]
&
J. Andrew McCammon‡ Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California at San Diego.Gilman Dr., Mail Code, 92093-0365, San Diego, CA, USA
Pages 45-61 | Received 01 Sep 2002, Accepted 01 Oct 2002, Published online: 15 Aug 2006

Citations (19)

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Ping Yu, Guo-zhen Zhu & Mao Wen. (2020) Application of grand-canonical ensemble Monte Carlo simulation in metals using cavity-biased method. Molecular Simulation 46:10, pages 736-742.
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Articles from other publishers (18)

Gregory A. Ross, Ariën S. Rustenburg, Patrick B. Grinaway, Josh Fass & John D. Chodera. (2018) Biomolecular Simulations under Realistic Macroscopic Salt Conditions. The Journal of Physical Chemistry B 122:21, pages 5466-5486.
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Justin A. Lemkul, Sirish Kaushik Lakkaraju & Alexander D. MacKerellJr.Jr.. (2016) Characterization of Mg 2+ Distributions around RNA in Solution . ACS Omega 1:4, pages 680-688.
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Daniel M. Hinckley & Juan J. de Pablo. (2015) Coarse-Grained Ions for Nucleic Acid Modeling. Journal of Chemical Theory and Computation 11:11, pages 5436-5446.
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Jaydeep P Bardhan. (2012) Biomolecular electrostatics—I want your solvation (model). Computational Science & Discovery 5:1, pages 013001.
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Albert H. Mao & Rohit V. Pappu. (2012) Crystal lattice properties fully determine short-range interaction parameters for alkali and halide ions. The Journal of Chemical Physics 137:6.
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Bob Eisenberg. 2011. Advances in Chemical Physics. Advances in Chemical Physics 77 223 .
Zhan Chen, Nathan A. Baker & G. W. Wei. (2011) Differential geometry based solvation model II: Lagrangian formulation. Journal of Mathematical Biology 63:6, pages 1139-1200.
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Zhan Chen, Nathan A. Baker & G.W. Wei. (2010) Differential geometry based solvation model I: Eulerian formulation. Journal of Computational Physics 229:22, pages 8231-8258.
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Attila Malasics & Dezső Boda. (2010) An efficient iterative grand canonical Monte Carlo algorithm to determine individual ionic chemical potentials in electrolytes. The Journal of Chemical Physics 132:24, pages 244103.
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Andreas Vitalis & Rohit V. Pappu. (2009) ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions. Journal of Computational Chemistry 30:5, pages 673-699.
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Alan A. Chen, Marcelo Marucho, Nathan A. Baker & Rohit V. Pappu. 2009. Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: Part B. Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: Part B 411 432 .
David S. Cerutti, Isolde Le Trong, Ronald E. Stenkamp & Terry P. Lybrand. (2008) Simulations of a Protein Crystal: Explicit Treatment of Crystallization Conditions Links Theory and Experiment in the Streptavidin−Biotin Complex. Biochemistry 47:46, pages 12065-12077.
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Attila Malasics, Dirk Gillespie & Dezső Boda. (2008) Simulating prescribed particle densities in the grand canonical ensemble using iterative algorithms. The Journal of Chemical Physics 128:12.
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Paweł Grochowski & Joanna Trylska. (2008) Continuum molecular electrostatics, salt effects, and counterion binding—A review of the Poisson–Boltzmann theory and its modifications. Biopolymers 89:2, pages 93-113.
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Feng Dong, Jason A. Wagoner & Nathan A. Baker. (2008) Assessing the performance of implicit solvation models at a nucleic acid surface. Physical Chemistry Chemical Physics 10:32, pages 4889.
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John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco & Klaus Schulten. (2007) Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry 28:16, pages 2618-2640.
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Benzhuo Lu, Y. C. Zhou, Gary A. Huber, Stephen D. Bond, Michael J. Holst & J. Andrew McCammon. (2007) Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. The Journal of Chemical Physics 127:13.
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Scott A. Showalter, Nathan A. Baker, Changguo Tang & Kathleen B. Hall. (2005) Iron Responsive Element RNA Flexibility Described by NMR and Isotropic Reorientational Eigenmode Dynamics. Journal of Biomolecular NMR 32:3, pages 179-193.
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