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Dr Gerhard Koenig

Senior Research Fellow

  1. 2021
  2. Published

    Ensembler: a simple package for fast prototyping and teaching molecular simulations

    Benjamin Ries, Stephanie M. Linker, David F. Hahn, Dr Gerhard Koenig & Sereina Riniker, 29 Jan 2021, In: Journal of Chemical Information and Modeling. 61, 2, p. 560-564 5 p.

    Research output: Contribution to journalArticlepeer-review

  3. 2020
  4. Published

    On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces

    Dr Gerhard Koenig & Sereina Riniker, 6 Dec 2020, In: Interface Focus. 10, 6, 11 p., 20190121.

    Research output: Contribution to journalArticlepeer-review

  5. Published

    An alternative to conventional λ-intermediate states in alchemical free energy calculations: λ-enveloping distribution sampling

    Dr Gerhard Koenig, Nina Glaser, Benjamin Schroeder, Alžbeta Kubincová, Philippe H. Hünenberger & Sereina Riniker, 23 Nov 2020, In: Journal of Chemical Information and Modeling. 60, 11, p. 5407-5423 17 p.

    Research output: Contribution to journalArticlepeer-review

  6. Published

    Overcoming orthogonal barriers in alchemical free energy calculations: on the relative merits of λ-variations, λ-extrapolations, and biasing

    David F. Hahn, Dr Gerhard Koenig & Philippe H. Hünenberger, 10 Mar 2020, In: Journal of Chemical Theory and Computation. 16, 3, p. 1630-1645 16 p.

    Research output: Contribution to journalArticlepeer-review

  7. 2018
  8. Published

    A comparison of QM/MM simulations with and without the Drude oscillator model based on hydration free energies of simple solutes

    Dr Gerhard Koenig, Frank C. Pickard, Jing Huang, Walter Thiel, Alexander D. MacKerell, Bernard R. Brooks & Darrin M. York, 19 Oct 2018, In: Molecules. 23, 10, 2695.

    Research output: Contribution to journalArticlepeer-review

  9. Published

    On the convergence of multi-scale free energy simulations

    Dr Gerhard Koenig, Bernard R. Brooks, Walter Thiel & Darrin M. York, 22 Sep 2018, In: Molecular Simulation. 44, 13-14, p. 1062-1081 20 p.

    Research output: Contribution to journalArticlepeer-review

  10. Published

    1-Butanol as a solvent for efficient extraction of polar compounds from aqueous medium: theoretical and practical aspects

    Dr Gerhard Koenig, Manfred T. Reetz & Walter Thiel, 12 Jul 2018, In: Journal of Physical Chemistry B. 122, 27, p. 6975-6988 14 p.

    Research output: Contribution to journalArticlepeer-review

  11. 2017
  12. Published

    An estimation of hybrid quantum mechanical molecular mechanical polarization energies for small molecules using polarizable force-field approaches

    Jing Huang, Ye Mei, Dr Gerhard Koenig, Andrew C. Simmonett, Frank C. Pickard, Qin Wu, Lee Ping Wang, Alexander D. MacKerell, Bernard R. Brooks & Yihan Shao, 14 Feb 2017, In: Journal of Chemical Theory and Computation. 13, 2, p. 679-695 17 p.

    Research output: Contribution to journalArticlepeer-review

  13. Published

    Absolute binding free energies for octa-acids and guests in SAMPL5: evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge

    Florentina Tofoleanu, Juyong Lee, Frank C. Pickard IV, Dr Gerhard Koenig, Jing Huang, Minkyung Baek, Chaok Seok & Bernard R. Brooks, 1 Jan 2017, In: Journal of Computer-Aided Molecular Design. 31, 1, p. 107-118 12 p.

    Research output: Contribution to journalArticlepeer-review

  14. Published

    Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

    Juyong Lee, Florentina Tofoleanu, Frank C. Pickard, Dr Gerhard Koenig, Jing Huang, Ana Damjanović, Minkyung Baek, Chaok Seok & Bernard R. Brooks, 1 Jan 2017, In: Journal of Computer-Aided Molecular Design. 31, 1, p. 71-85 15 p.

    Research output: Contribution to journalArticlepeer-review

  15. 2016
  16. Published

    Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections

    Frank C. Pickard, Dr Gerhard Koenig, Florentina Tofoleanu, Juyong Lee, Andrew C. Simmonett, Yihan Shao, Jay W. Ponder & Bernard R. Brooks, 1 Nov 2016, In: Journal of Computer-Aided Molecular Design. 30, 11, p. 1087-1100 14 p.

    Research output: Contribution to journalArticlepeer-review

  17. Published

    Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge

    Dr Gerhard Koenig, Frank C. Pickard, Jing Huang, Andrew C. Simmonett, Florentina Tofoleanu, Juyong Lee, Pavlo O. Dral, Samarjeet Prasad, Michael Jones, Yihan Shao & 2 others, Walter Thiel & Bernard R. Brooks, 1 Nov 2016, In: Journal of Computer-Aided Molecular Design. 30, 11, p. 989-1006 18 p.

    Research output: Contribution to journalArticlepeer-review

  18. Published

    An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations

    Frank C. Pickard, Dr Gerhard Koenig, Andrew C. Simmonett, Yihan Shao & Bernard R. Brooks, 15 Oct 2016, In: Bioorganic and Medicinal Chemistry. 24, 20, p. 4988-4997 10 p.

    Research output: Contribution to journalArticlepeer-review

  19. Published

    Comparison of methods to reweight from classical molecular simulations to QM/MM potentials

    Eric C. Dybeck, Dr Gerhard Koenig, Bernard R. Brooks & Michael R. Shirts, 12 Apr 2016, In: Journal of Chemical Theory and Computation. 12, 4, p. 1466-1480 15 p.

    Research output: Contribution to journalArticlepeer-review

  20. Published

    Calculations of solvation free energy through energy reweighting from molecular mechanics to quantum mechanics

    Xiangyu Jia, Meiting Wang, Yihan Shao, Dr Gerhard Koenig, Bernard R. Brooks, John Z.H. Zhang & Ye Mei, 9 Feb 2016, In: Journal of Chemical Theory and Computation. 12, 2, p. 499-511 13 p.

    Research output: Contribution to journalArticlepeer-review

  21. Published

    Computation of hydration free energies using the multiple environment single system quantum mechanical/molecular mechanical method

    Dr Gerhard Koenig, Ye Mei, Frank C. Pickard, Andrew C. Simmonett, Benjamin T. Miller, John M. Herbert, H. Lee Woodcock, Bernard R. Brooks & Yihan Shao, 12 Jan 2016, In: Journal of Chemical Theory and Computation. 12, 1, p. 332-344 13 p.

    Research output: Contribution to journalArticlepeer-review

  22. 2015
  23. Published

    Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations

    Dr Gerhard Koenig & Bernard R. Brooks, 1 May 2015, In: Biochimica et Biophysica Acta - General Subjects. 1850, 5, p. 932-943 12 p.

    Research output: Contribution to journalArticlepeer-review

  24. Published

    Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

    Alexander J. Sodt, Ye Mei, Dr Gerhard Koenig, Peng Tao, Ryan P. Steele, Bernard R. Brooks & Yihan Shao, 5 Mar 2015, In: Journal of Physical Chemistry A. 119, 9, p. 1511-1523 13 p.

    Research output: Contribution to journalArticlepeer-review

  25. 2014
  26. Published

    Computing the free energy along a reaction coordinate using rigid body dynamics

    Peng Tao, Alexander J. Sodt, Yihan Shao, Dr Gerhard Koenig & Bernard R. Brooks, 14 Oct 2014, In: Journal of Chemical Theory and Computation. 10, 10, p. 4198-4207 10 p.

    Research output: Contribution to journalArticlepeer-review

  27. Published

    Multiscale free energy simulations: an efficient method for connecting classical MD simulations to QM or QM/MM free energies using non-Boltzmann Bennett reweighting schemes

    Dr Gerhard Koenig, Phillip S. Hudson, Stefan Boresch & H. Lee Woodcock, 8 Apr 2014, In: Journal of Chemical Theory and Computation. 10, 4, p. 1406-1419 14 p.

    Research output: Contribution to journalArticlepeer-review

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