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There are 9917 results for: content related to: Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module

  1. GROMACS: Fast, flexible, and free

    Journal of Computational Chemistry

    Volume 26, Issue 16, December 2005, Pages: 1701–1718, David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark and Herman J. C. Berendsen

    Version of Record online : 6 OCT 2005, DOI: 10.1002/jcc.20291

  2. You have full text access to this OnlineOpen article
    Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

    Journal of Computational Chemistry

    Volume 36, Issue 26, October 5, 2015, Pages: 1990–2008, Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot and Helmut Grubmüller

    Version of Record online : 4 AUG 2015, DOI: 10.1002/jcc.24030

  3. Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5

    Journal of Computational Chemistry

    Volume 32, Issue 9, 15 July 2011, Pages: 2031–2040, Mark J. Abraham and Jill E. Gready

    Version of Record online : 5 APR 2011, DOI: 10.1002/jcc.21773

  4. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model

    Journal of Computational Chemistry

    Volume 36, Issue 19, July 15, 2015, Pages: 1473–1479, Justin A. Lemkul, Benoît Roux, David van der Spoel and Alexander D. MacKerell Jr.

    Version of Record online : 12 MAY 2015, DOI: 10.1002/jcc.23937

  5. Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds

    Biotechnology and Applied Biochemistry

    Monikaben Padariya, Umesh Kalathiya and Maciej Baginski

    Version of Record online : 17 MAY 2017, DOI: 10.1002/bab.1543

  6. GROMACS—the road ahead

    Wiley Interdisciplinary Reviews: Computational Molecular Science

    Volume 1, Issue 5, September/October 2011, Pages: 710–715, David van der Spoel and Berk Hess

    Version of Record online : 25 APR 2011, DOI: 10.1002/wcms.50

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    OBGMX: A web-based generator of GROMACS topologies for molecular and periodic systems using the universal force field

    Journal of Computational Chemistry

    Volume 33, Issue 27, 15 October 2012, Pages: 2204–2208, Giovanni Garberoglio

    Version of Record online : 20 JUN 2012, DOI: 10.1002/jcc.23049

  8. The measured and calculated affinity of methyl- and methoxy-substituted benzoquinones for the QA site of bacterial reaction centers

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 12, September 2010, Pages: 2638–2654, Zhong Zheng, P. Leslie Dutton and M. R. Gunner

    Version of Record online : 1 JUN 2010, DOI: 10.1002/prot.22779

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    Performance enhancements for GROMACS nonbonded interactions on BlueGene

    Journal of Computational Chemistry

    Volume 32, Issue 9, 15 July 2011, Pages: 2041–2046, Mark J. Abraham

    Version of Record online : 5 APR 2011, DOI: 10.1002/jcc.21766

  10. Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities

    Journal of Computational Chemistry

    Volume 32, Issue 4, March 2011, Pages: 600–606, Christian C. Gruber and Jürgen Pleiss

    Version of Record online : 1 SEP 2010, DOI: 10.1002/jcc.21645

  11. Gro2mat: A package to efficiently read gromacs output in MATLAB

    Journal of Computational Chemistry

    Volume 35, Issue 20, July 30, 2014, Pages: 1528–1531, Hung Dien, Charlotte M. Deane and Bernhard Knapp

    Version of Record online : 12 JUN 2014, DOI: 10.1002/jcc.23650

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    pmx: Automated protein structure and topology generation for alchemical perturbations

    Journal of Computational Chemistry

    Volume 36, Issue 5, February 15, 2015, Pages: 348–354, Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger and Bert L. de Groot

    Version of Record online : 8 DEC 2014, DOI: 10.1002/jcc.23804

  13. An assessment of the accuracy of methods for predicting hydrogen positions in protein structures

    Proteins: Structure, Function, and Bioinformatics

    Volume 61, Issue 2, 1 November 2005, Pages: 296–309, Lucy R. Forrest and Barry Honig

    Version of Record online : 19 AUG 2005, DOI: 10.1002/prot.20601

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    Speeding up parallel GROMACS on high-latency networks

    Journal of Computational Chemistry

    Volume 28, Issue 12, September 2007, Pages: 2075–2084, Carsten Kutzner, David Van Der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. De Groot and Helmut Grubmüller

    Version of Record online : 2 APR 2007, DOI: 10.1002/jcc.20703

  15. Accuracy assessment of the linear Poisson–Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid–protein complexes

    Journal of Computational Chemistry

    Volume 36, Issue 9, April 5, 2015, Pages: 585–596, Federico Fogolari, Alessandra Corazza and Gennaro Esposito

    Version of Record online : 8 JAN 2015, DOI: 10.1002/jcc.23832

  16. New QM/MM implementation of the DFTB3 method in the gromacs package

    Journal of Computational Chemistry

    Volume 36, Issue 26, October 5, 2015, Pages: 1978–1989, Tomáš Kubař, Kai Welke and Gerrit Groenhof

    Version of Record online : 4 AUG 2015, DOI: 10.1002/jcc.24029

  17. Combination of the CHARMM27 force field with united-atom lipid force fields

    Journal of Computational Chemistry

    Volume 32, Issue 7, May 2011, Pages: 1400–1410, Nicolas Sapay and D. Peter Tieleman

    Version of Record online : 31 DEC 2010, DOI: 10.1002/jcc.21726

  18. Comparison of Thermodynamic Properties of Coarse-Grained and Atomic-Level Simulation Models

    ChemPhysChem

    Volume 8, Issue 3, February 19, 2007, Pages: 452–461, Riccardo Baron, Daniel Trzesniak, Alex H. de Vries , Andreas Elsener, Siewert J. Marrink and Wilfred F. van Gunsteren

    Version of Record online : 8 FEB 2007, DOI: 10.1002/cphc.200600658

  19. SwissParam: A fast force field generation tool for small organic molecules

    Journal of Computational Chemistry

    Volume 32, Issue 11, August 2011, Pages: 2359–2368, Vincent Zoete, Michel A. Cuendet, Aurélien Grosdidier and Olivier Michielin

    Version of Record online : 3 MAY 2011, DOI: 10.1002/jcc.21816

  20. Development of a multipoint model for sulfur in proteins: A new parametrization scheme to reproduce high-level ab initio interaction energies

    Journal of Computational Chemistry

    Volume 26, Issue 3, February 2005, Pages: 283–293, F. Wennmohs and M. Schindler

    Version of Record online : 21 DEC 2004, DOI: 10.1002/jcc.20163