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There are 17916 results for: content related to: On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations

  1. A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers

    Journal of Computational Chemistry

    Volume 32, Issue 6, 30 April 2011, Pages: 998–1032, Halvor S. Hansen and Philippe H. Hünenberger

    Version of Record online : 10 NOV 2010, DOI: 10.1002/jcc.21675

  2. A Molecular Dynamics Study of the ASC and NALP1 Pyrin Domains at Neutral and Low pH

    ChemBioChem

    Volume 9, Issue 6, April 14, 2008, Pages: 923–933, Zrinka Gattin and Wilfred F. van Gunsteren

    Version of Record online : 17 MAR 2008, DOI: 10.1002/cbic.200700434

  3. Computational Characterization of Reaction Intermediates in the Photocycle of the Sensory Domain of the AppA Blue Light Photoreceptor

    Photochemistry and Photobiology

    Volume 87, Issue 3, May/June 2011, Pages: 564–573, Maria G. Khrenova, Tatiana Domratcheva, Ilme Schlichting, Bella L. Grigorenko and Alexander V. Nemukhin

    Version of Record online : 13 DEC 2010, DOI: 10.1111/j.1751-1097.2010.00861.x

  4. Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and chloroform-to-water partition coefficients

    Journal of Computational Chemistry

    Volume 33, Issue 28, 30 October 2012, Pages: 2225–2232, Maarten G. Wolf and Gerrit Groenhof

    Version of Record online : 10 JUL 2012, DOI: 10.1002/jcc.23055

  5. Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol

    Journal of Computational Chemistry

    Volume 33, Issue 24, 15 September 2012, Pages: 1907–1917, Bruno A. C. Horta, Zhixiong Lin, Wei Huang, Sereina Riniker, Wilfred F. van Gunsteren and Philippe H. Hünenberger

    Version of Record online : 30 MAY 2012, DOI: 10.1002/jcc.23021

  6. You have full text access to this OnlineOpen article
    The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

    Journal of Computational Chemistry

    Volume 36, Issue 9, April 5, 2015, Pages: 633–648, Letif Mones, Andrew Jones, Andreas W. Götz, Teodoro Laino, Ross C. Walker, Ben Leimkuhler, Gábor Csányi and Noam Bernstein

    Version of Record online : 3 FEB 2015, DOI: 10.1002/jcc.23839

  7. Application of a BOSS—Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions

    Journal of Computational Chemistry

    Volume 36, Issue 27, October 15, 2015, Pages: 2064–2074, Jonah Z. Vilseck, Jakub Kostal, Julian Tirado-Rives and William L. Jorgensen

    Version of Record online : 27 AUG 2015, DOI: 10.1002/jcc.24045

  8. QM/MM study of the absorption spectra of DsRed.M1 chromophores

    Journal of Computational Chemistry

    Volume 31, Issue 8, June 2010, Pages: 1603–1612, Elsa Sanchez-Garcia, Markus Doerr and Walter Thiel

    Version of Record online : 14 DEC 2009, DOI: 10.1002/jcc.21443

  9. Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations

    Proteins: Structure, Function, and Bioinformatics

    Volume 66, Issue 2, 1 February 2007, Pages: 456–466, Bella L. Grigorenko, Alexander V. Nemukhin, Maria S. Shadrina, Igor A. Topol and Stanley K. Burt

    Version of Record online : 8 NOV 2006, DOI: 10.1002/prot.21228

  10. A new GROMOS force field for hexopyranose-based carbohydrates

    Journal of Computational Chemistry

    Volume 26, Issue 13, October 2005, Pages: 1400–1412, Roberto D. Lins and Philippe H. Hünenberger

    Version of Record online : 20 JUL 2005, DOI: 10.1002/jcc.20275

  11. Contributions of pauli repulsions to the energetics and physical properties computed in QM/MM methods

    Journal of Computational Chemistry

    Volume 34, Issue 27, 15 October 2013, Pages: 2380–2388, Yingdi Jin, Erin R. Johnson, Xiangqian Hu, Weitao Yang and Hao Hu

    Version of Record online : 6 AUG 2013, DOI: 10.1002/jcc.23401

  12. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

    Journal of Computational Chemistry

    Volume 23, Issue 14, 15 November 2002, Pages: 1314–1322, Stephen J. Titmuss, Peter L. Cummins, Alistair P. Rendell, Andrey A. Bliznyuk and Jill E. Gready

    Version of Record online : 13 AUG 2002, DOI: 10.1002/jcc.10122

  13. QM/MM through the 1990s: The First Twenty Years of Method Development and Applications

    Israel Journal of Chemistry

    Volume 54, Issue 8-9, August 2014, Pages: 1250–1263, Meiyi Liu, Yingjie Wang, Yakun Chen, Martin J. Field and Jiali Gao

    Version of Record online : 31 JUL 2014, DOI: 10.1002/ijch.201400036

  14. QM/MM Methods for Biomolecular Systems

    Angewandte Chemie International Edition

    Volume 48, Issue 7, February 2, 2009, Pages: 1198–1229, Hans Martin Senn and Walter Thiel

    Version of Record online : 28 JAN 2009, DOI: 10.1002/anie.200802019

  15. You have full text access to this OnlineOpen article
    ChemShell—a modular software package for QM/MM simulations

    Wiley Interdisciplinary Reviews: Computational Molecular Science

    Volume 4, Issue 2, March/April 2014, Pages: 101–110, Sebastian Metz, Johannes Kästner, Alexey A. Sokol, Thomas W. Keal and Paul Sherwood

    Version of Record online : 19 JUL 2013, DOI: 10.1002/wcms.1163

  16. Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI)

    Journal of Computational Chemistry

    Volume 36, Issue 25, September 30, 2015, Pages: 1859–1873, Pin-Chih Su, Cheng-Chieh Tsai, Shahila Mehboob, Kirk E. Hevener and Michael E. Johnson

    Version of Record online : 27 JUL 2015, DOI: 10.1002/jcc.24011

  17. Unique QM/MM potential energy surface exploration using microiterations

    International Journal of Quantum Chemistry

    Volume 111, Issue 13, 5 November 2011, Pages: 3339–3346, Federico Melaccio, Massimo Olivucci, Roland Lindh and Nicolas Ferré

    Version of Record online : 25 APR 2011, DOI: 10.1002/qua.23067

  18. Quantum Mechanical/Molecular Mechanical (QM/MM) Methods and Applictions in Bioinorganic Chemistry

    Standard Article

    Encyclopedia of Inorganic Chemistry

    Ulf Ryde

    Published Online : 15 SEP 2009, DOI: 10.1002/0470862106.ia606

  19. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6

    Journal of Computational Chemistry

    Volume 25, Issue 13, October 2004, Pages: 1656–1676, Chris Oostenbrink, Alessandra Villa, Alan E. Mark and Wilfred F. Van Gunsteren

    Version of Record online : 14 JUL 2004, DOI: 10.1002/jcc.20090

  20. An extensible interface for QM/MM molecular dynamics simulations with AMBER

    Journal of Computational Chemistry

    Volume 35, Issue 2, 15 January 2014, Pages: 95–108, Andreas W. Götz, Matthew A. Clark and Ross C. Walker

    Version of Record online : 9 OCT 2013, DOI: 10.1002/jcc.23444