Journal of Chemical Theory and Computation

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  • 2025 Journal Article
    ​ ​Constant pH Simulation with FMM Electrostatics in GROMACS. (B) GPU Accelerated Hamiltonian Interpolation​
    Kohnke, B.; Briand, E.; Kutzner, C. & Grubmüller, H.​ (2025) 
    Journal of Chemical Theory and Computation21(4) pp. 1787​-1804​.​ DOI: https://doi.org/10.1021/acs.jctc.4c01319 
    Details  DOI 
  • 2025 Journal Article
    ​ ​Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications​
    Briand, E.; Kohnke, B.; Kutzner, C. & Grubmüller, H.​ (2025) 
    Journal of Chemical Theory and Computation21(4) pp. 1762​-1786​.​ DOI: https://doi.org/10.1021/acs.jctc.4c01318 
    Details  DOI 
  • 2024 Journal Article
    ​ ​Guidelines for Free-Energy Calculations Involving Charge Changes​
    Petrov, D.; Perthold, J. W.; Oostenbrink, C.; de Groot, B. L. & Gapsys, V.​ (2024) 
    Journal of Chemical Theory and Computation20(2) pp. 914​-925​.​ DOI: https://doi.org/10.1021/acs.jctc.3c00757 
    Details  DOI 
  • 2024 Journal Article
    ​ ​Local Electronic Correlation in Multicomponent Møller–Plesset Perturbation Theory​
    Hasecke, L. & Mata, R. A.​ (2024) 
    Journal of Chemical Theory and Computation20(22) pp. 9928​-9938​.​ DOI: https://doi.org/10.1021/acs.jctc.4c01059 
    Details  DOI 
  • 2023 Journal Article
    ​ ​Accurate Fourth-Generation Machine Learning Potentials by Electrostatic Embedding​
    Ko, T. W.; Finkler, J. A.; Goedecker, S. & Behler, J.​ (2023) 
    Journal of Chemical Theory and Computation19(12) pp. 3567​-3579​.​ DOI: https://doi.org/10.1021/acs.jctc.2c01146 
    Details  DOI 
  • 2023 Journal Article
    ​ ​Learning Conductance: Gaussian Process Regression for Molecular Electronics​
    Deffner, M.; Weise, M. P.; Zhang, H.; Mücke, M.; Proppe, J.; Franco, I. & Herrmann, C.​ (2023) 
    Journal of Chemical Theory and Computation19(3) pp. 992​-1002​.​ DOI: https://doi.org/10.1021/acs.jctc.2c00648 
    Details  DOI 
  • 2023 Journal Article
    ​ ​Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field​
    Boothroyd, S.; Behara, P. K.; Madin, O. C.; Hahn, D. F.; Jang, H.; Gapsys, V. & Wagner, J. R. et al.​ (2023) 
    Journal of Chemical Theory and Computation, art. acs.jctc.3c00039​.​ DOI: https://doi.org/10.1021/acs.jctc.3c00039 
    Details  DOI 
  • 2023 Journal Article
    ​ ​Accurately Predicting Protein p K a Values Using Nonequilibrium Alchemy​
    Wilson, C. J.; Karttunen, M.; de Groot, B. L. & Gapsys, V.​ (2023) 
    Journal of Chemical Theory and Computation, art. acs.jctc.3c00721​.​ DOI: https://doi.org/10.1021/acs.jctc.3c00721 
    Details  DOI 
  • 2023 Journal Article
    ​ ​CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization​
    Stroh, K. S.; Souza, P. C. T.; Monticelli, L. & Risselada, H. J.​ (2023) 
    Journal of Chemical Theory and Computation19(22) pp. 8384​-8400​.​ DOI: https://doi.org/10.1021/acs.jctc.3c00637 
    Details  DOI 
  • 2023 Journal Article
    ​ ​Why Solvent Response Contributions to Solvation Free Energies Are Compatible with Ben-Naim’s Theorem​
    Heinz, L. P. & Grubmüller, H.​ (2023) 
    Journal of Chemical Theory and Computation19(22) pp. 8013​-8019​.​ DOI: https://doi.org/10.1021/acs.jctc.3c00655 
    Details  DOI 
  • 2023 Journal Article
    ​ ​Ion Conduction Mechanisms in Potassium Channels Revealed by Permeation Cycles​
    Lam, C. K. & de Groot, B. L.​ (2023) 
    Journal of Chemical Theory and Computation, art. acs.jctc.3c00061​.​ DOI: https://doi.org/10.1021/acs.jctc.3c00061 
    Details  DOI 
  • 2023 Journal Article
    ​ ​Uncertainties in Markov State Models of Small Proteins​
    Kozlowski, N. & Grubmüller, H.​ (2023) 
    Journal of Chemical Theory and Computation19(16) pp. 5516​-5524​.​ DOI: https://doi.org/10.1021/acs.jctc.3c00372 
    Details  DOI 
  • 2023 Journal Article | 
    ​ ​Nuclear Quantum Effects Made Accessible: Local Density Fitting in Multicomponent Methods​
    Hasecke, L. & Mata, R. A.​ (2023) 
    Journal of Chemical Theory and Computation19(22) pp. 8223​-8233​.​ DOI: https://doi.org/10.1021/acs.jctc.3c01055 
    Details  DOI 
  • 2022 Journal Article
    ​ ​Efficient Quantification of Lipid Packing Defect Sensing by Amphipathic Peptides: Comparing Martini 2 and 3 with CHARMM36​
    van Hilten, N.; Stroh, K. S. & Risselada, H. J.​ (2022) 
    Journal of Chemical Theory and Computation, art. acs.jctc.2c00222​.​ DOI: https://doi.org/10.1021/acs.jctc.2c00222 
    Details  DOI 
  • 2022 Journal Article | 
    ​ ​Chemical Space Exploration with Active Learning and Alchemical Free Energies​
    Khalak, Y.; Tresadern, G.; Hahn, D. F.; de Groot, B. L.   & Gapsys, V. ​ (2022) 
    Journal of Chemical Theory and Computation, art. acs.jctc.2c00752​.​ DOI: https://doi.org/10.1021/acs.jctc.2c00752 
    Details  DOI 
  • 2021 Journal Article | Research Paper | 
    ​ ​Time-Lagged Independent Component Analysis of Random Walks and Protein Dynamics​
    Schultze, S. & Grubmüller, H. ​ (2021) 
    Journal of chemical theory and computation17(9) pp. 5766​-5776​.​ DOI: https://doi.org/10.1021/acs.jctc.1c00273 
    Details  DOI  PMID  PMC 
  • 2021 Journal Article
    ​ ​Quantifying Membrane Curvature Sensing of Peripheral Proteins by Simulated Buckling and Umbrella Sampling​
    Stroh, K. S. & Risselada, H. J.​ (2021) 
    Journal of Chemical Theory and Computation17(8) pp. 5276​-5286​.​ DOI: https://doi.org/10.1021/acs.jctc.1c00021 
    Details  DOI 
  • 2021 Journal Article
    ​ ​ATP–Magnesium Coordination: Protein Structure-Based Force Field Evaluation and Corrections​
    Buelens, F. P.; Leonov, H.; de Groot, B. L.   & Grubmüller, H. ​ (2021) 
    Journal of Chemical Theory and Computation17(3) pp. 1922​-1930​.​ DOI: https://doi.org/10.1021/acs.jctc.0c01205 
    Details  DOI 
  • 2021 Journal Article
    ​ ​Per​
    Heinz, L. P. & Grubmüller, H. ​ (2021) 
    Journal of Chemical Theory and Computation17(4) pp. 2090​-2098​.​ DOI: https://doi.org/10.1021/acs.jctc.0c00961 
    Details  DOI 
  • 2020 Journal Article
    ​ ​Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides​
    Dobrev, P.; Vemulapalli, S. P. B.; Nath, N. ; Griesinger, C.   & Grubmüller, H. ​ (2020) 
    Journal of Chemical Theory and Computation16(4) pp. 2561​-2569​.​ DOI: https://doi.org/10.1021/acs.jctc.9b01232 
    Details  DOI 
  • 2020 Journal Article | Erratum
    ​ ​Correction to “Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides”​
    Dobrev, P.; Vemulapalli, S. P. B.; Nath, N. ; Griesinger, C. ; Groenhof, G.   & Grubmüller, H. ​ (2020) 
    Journal of Chemical Theory and Computation16(7) pp. 4753​-4753​.​ DOI: https://doi.org/10.1021/acs.jctc.0c00500 
    Details  DOI 
  • 2020 Journal Article
    ​ ​Determining Free-Energy Differences Through Variationally Derived Intermediates​
    Reinhardt, M. & Grubmüller, H. ​ (2020) 
    Journal of Chemical Theory and Computation16(6) pp. 3504​-3512​.​ DOI: https://doi.org/10.1021/acs.jctc.0c00106 
    Details  DOI 
  • 2020 Journal Article
    ​ ​A GPU-Accelerated Fast Multipole Method for GROMACS: Performance and Accuracy​
    Kohnke, B.; Kutzner, C. & Grubmüller, H. ​ (2020) 
    Journal of Chemical Theory and Computation16(11) pp. 6938​-6949​.​ DOI: https://doi.org/10.1021/acs.jctc.0c00744 
    Details  DOI 
  • 2019 Journal Article
    ​ ​Library-Based LAMMPS Implementation of High-Dimensional Neural Network Potentials​
    Singraber, A.; Behler, J.   & Dellago, C.​ (2019) 
    Journal of Chemical Theory and Computation15(3) pp. 1827​-1840​.​ DOI: https://doi.org/10.1021/acs.jctc.8b00770 
    Details  DOI 
  • 2019 Journal Article
    ​ ​From Molecular Fragments to the Bulk: Development of a Neural Network Potential for MOF-5​
    Eckhoff, M. & Behler, J. ​ (2019) 
    Journal of Chemical Theory and Computation15(6) pp. 3793​-3809​.​ DOI: https://doi.org/10.1021/acs.jctc.8b01288 
    Details  DOI 
  • 2019 Journal Article
    ​ ​Parallel Multistream Training of High-Dimensional Neural Network Potentials​
    Singraber, A.; Morawietz, T.; Behler, J.   & Dellago, C.​ (2019) 
    Journal of Chemical Theory and Computation15(5) pp. 3075​-3092​.​ DOI: https://doi.org/10.1021/acs.jctc.8b01092 
    Details  DOI 
  • 2019 Journal Article
    ​ ​Combined Small-Angle X-ray and Neutron Scattering Restraints in Molecular Dynamics Simulations​
    Chen, P.-c.; Shevchuk, R.; Strnad, F. M.; Lorenz, C.; Karge, L.; Gilles, R. & Stadler, A. M. et al.​ (2019) 
    Journal of Chemical Theory and Computation15(8) pp. 4687​-4698​.​ DOI: https://doi.org/10.1021/acs.jctc.9b00292 
    Details  DOI 
  • 2019 Journal Article
    ​ ​SAXS-Restrained Ensemble Simulations of Intrinsically Disordered Proteins with Commitment to the Principle of Maximum Entropy​
    Hermann, M. R. & Hub, J. S. ​ (2019) 
    Journal of Chemical Theory and Computation15(9) pp. 5103​-5115​.​ DOI: https://doi.org/10.1021/acs.jctc.9b00338 
    Details  DOI 
  • 2019 Journal Article
    ​ ​Automated Fitting of Neural Network Potentials at Coupled Cluster Accuracy: Protonated Water Clusters as Testing Ground​
    Schran, C.; Behler, J.   & Marx, D.​ (2019) 
    Journal of Chemical Theory and Computation16(1) pp. 88​-99​.​ DOI: https://doi.org/10.1021/acs.jctc.9b00805 
    Details  DOI 
  • 2019 Journal Article
    ​ ​SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures​
    Nagy, G.; Igaev, M.; Jones, N. C.; Hoffmann, S. V. & Grubmüller, H. ​ (2019) 
    Journal of Chemical Theory and Computation15(9) pp. 5087​-5102​.​ DOI: https://doi.org/10.1021/acs.jctc.9b00203 
    Details  DOI 
  • 2019 Journal Article
    ​ ​Computing Spatially Resolved Rotational Hydration Entropies from Atomistic Simulations​
    Heinz, L. P. & Grubmüller, H. ​ (2019) 
    Journal of Chemical Theory and Computation16(1) pp. 108​-118​.​ DOI: https://doi.org/10.1021/acs.jctc.9b00926 
    Details  DOI 
  • 2019 Journal Article
    ​ ​Limits of Coupled-Cluster Calculations for Non-Heme Iron Complexes​
    Feldt, M.; Phung, Q. M.; Pierloot, K.; Mata, R. A.   & Harvey, J. N.​ (2019) 
    Journal of Chemical Theory and Computation15(2) pp. 922​-937​.​ DOI: https://doi.org/10.1021/acs.jctc.8b00963 
    Details  DOI  PMID  PMC 
  • 2018 Journal Article
    ​ ​Universal Method for Electrostatic Interaction Energies Estimation with Charge Penetration and Easily Attainable Point Charges​
    Bojarowski, S. A.; Kumar, P.; Wandtke, C. M.; Dittrich, B.   & Dominiak, P. M.​ (2018) 
    Journal of Chemical Theory and Computation14(12) pp. 6336​-6345​.​ DOI: https://doi.org/10.1021/acs.jctc.8b00781 
    Details  DOI 
  • 2018 Journal Article
    ​ ​Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations​
    Bastys, T.; Gapsys, V. ; Doncheva, N. T.; Kaiser, R.; de Groot, B. L.   & Kalinina, O. V.​ (2018) 
    Journal of Chemical Theory and Computation14(7) pp. 3397​-3408​.​ DOI: https://doi.org/10.1021/acs.jctc.7b01109 
    Details  DOI 
  • 2018 Journal Article
    ​ ​Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field​
    Olesen, K.; Awasthi, N.; Bruhn, D. S.; Pezeshkian, W. & Khandelia, H.​ (2018) 
    Journal of Chemical Theory and Computation14(6) pp. 3342​-3350​.​ DOI: https://doi.org/10.1021/acs.jctc.8b00267 
    Details  DOI 
  • 2018 Journal Article
    ​ ​Interpretation of Interfacial Protein Spectra with Enhanced Molecular Simulation Ensembles​
    Lutz, H.; Jaeger, V.; Weidner, T. & de Groot, B. L. ​ (2018) 
    Journal of Chemical Theory and Computation15(1) pp. 698​-707​.​ DOI: https://doi.org/10.1021/acs.jctc.8b00840 
    Details  DOI 
  • 2018 Journal Article
    ​ ​Hybrid Local Molecular Orbital: Molecular Orbital Calculations for Open Shell Systems​
    Feldt, M. & Mata, R. A. ​ (2018) 
    Journal of Chemical Theory and Computation14(10) pp. 5192​-5202​.​ DOI: https://doi.org/10.1021/acs.jctc.8b00727 
    Details  DOI  PMID  PMC 
  • 2017 Journal Article
    ​ ​Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes​
    Gapsys, V.   & de Groot, B. L. ​ (2017) 
    Journal of Chemical Theory and Computation13(12) pp. 6275​-6289​.​ DOI: https://doi.org/10.1021/acs.jctc.7b00849 
    Details  DOI 
  • 2017 Journal Article
    ​ ​Probing a Continuous Polar Defect: A Reaction Coordinate for Pore Formation in Lipid Membranes​
    Hub, J. S. & Awasthi, N.​ (2017) 
    Journal of Chemical Theory and Computation13(5) pp. 2352​-2366​.​ DOI: https://doi.org/10.1021/acs.jctc.7b00106 
    Details  DOI  PMID  PMC  WoS 
  • 2017 Journal Article
    ​ ​Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pK(a) Calculations​
    Dobrev, P.; Donnini, S.; Groenhof, G.   & Grubmüller, H. ​ (2017) 
    Journal of chemical theory and computation13(1) pp. 147​-160​.​ DOI: https://doi.org/10.1021/acs.jctc.6b00807 
    Details  DOI  PMID  PMC 
  • 2016 Journal Article
    ​ ​Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer​
    Donnini, S.; Ullmann, R. T.; Groenhof, G.   & Grubmüller, H. ​ (2016) 
    Journal of Chemical Theory and Computation12(3) pp. 1040​-1051​.​ DOI: https://doi.org/10.1021/acs.jctc.5b01160 
    Details  DOI  PMID  PMC 
  • 2016 Journal Article
    ​ ​Error-Safe, Portable, and Efficient Evolutionary Algorithms Implementation with High Scalability​
    Dieterich, J. M. & Hartke, B.​ (2016) 
    Journal of Chemical Theory and Computation12(10) pp. 5226​-5233​.​ DOI: https://doi.org/10.1021/acs.jctc.6b00716 
    Details  DOI  PMID  PMC  WoS 
  • 2016 Journal Article
    ​ ​Simulations of Pore Formation in Lipid Membranes: Reaction Coordinates, Convergence, Hysteresis, and Finite-Size Effects​
    Awasthi, N. & Hub, J. S.​ (2016) 
    Journal of Chemical Theory and Computation12(7) pp. 3261​-3269​.​ DOI: https://doi.org/10.1021/acs.jctc.6b00369 
    Details  DOI  PMID  PMC  WoS 
  • 2015 Journal Article | Research Paper
    ​ ​Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment​
    Rauscher, S.; Gapsys, V. ; Gajda, M. J.; Zweckstetter, M. ; Groot, B. L. de   & Grubmüller, H. ​ (2015) 
    Journal of Chemical Theory and Computation11(11) pp. 5513​-5524​.​ DOI: https://doi.org/10.1021/acs.jctc.5b00736 
    Details  DOI  PMID  PMC  WoS 
  • 2014 Journal Article
    ​ ​AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations​
    Graen, T.; Hoefling, M. & Grubmüller, H. ​ (2014) 
    Journal of Chemical Theory and Computation10(12) pp. 5505​-5512​.​ DOI: https://doi.org/10.1021/ct500869p 
    Details  DOI 
  • 2014 Journal Article | Research Paper
    ​ ​Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge​
    Hub, J. S. ; Groot, B. L. de ; Grubmüller, H.   & Groenhof, G. ​ (2014) 
    Journal of Chemical Theory and Computation10(1) pp. 381​-390​.​ DOI: https://doi.org/10.1021/ct400626b 
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  • 2014 Journal Article
    ​ ​Local Hybrid QM/QM Calculations of Reaction Pathways in Metallobiosites​
    Andrejic, M. & Mata, R. A.​ (2014) 
    Journal of Chemical Theory and Computation10(12) pp. 5397​-5404​.​ DOI: https://doi.org/10.1021/ct5008313 
    Details  DOI  PMID  PMC  WoS 
  • 2013 Journal Article | Erratum
    ​ ​Correction to Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics​
    Donnini, S.; Tegeler, F. ; Groenhof, G.   & Grubmüller, H. ​ (2013) 
    Journal of Chemical Theory and Computation9(7) pp. 3261​-3261​.​ DOI: https://doi.org/10.1021/ct400439g 
    Details  DOI 
  • 2013 Journal Article
    ​ ​Estimation of Interaction Potentials through the Configurational Temperature Formalism​
    Mechelke, M. & Habeck, M. ​ (2013) 
    Journal of Chemical Theory and Computation9(12) pp. 5685​-5692​.​ DOI: https://doi.org/10.1021/ct400580p 
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  • 2013 Journal Article
    ​ ​Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction​
    Li, J.-L.; Mata, R. A.   & Ryde, U.​ (2013) 
    Journal of Chemical Theory and Computation9(3) pp. 1799​-1807​.​ DOI: https://doi.org/10.1021/ct301094r 
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  • 2012 Journal Article
    ​ ​New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations​
    Gapsys, V. ; Seeliger, D. & de Groot, B. L. ​ (2012) 
    Journal of Chemical Theory and Computation8(7) pp. 2373​-2382​.​ DOI: https://doi.org/10.1021/ct300220p 
    Details  DOI 
  • 2012 Journal Article
    ​ ​Application of local second-order Møller-plesset perturbation theory to the study of structures in solution​
    Dieterich, J. M.; Oliveira, J. C. A. & Mata, R. A. ​ (2012) 
    Journal of Chemical Theory and Computation8(9) pp. 3053​-3060​.​ DOI: https://doi.org/10.1021/ct300009n 
    Details  DOI  PMID  PMC  WoS 
  • 2011 Journal Article
    ​ ​Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics​
    Donnini, S.; Tegeler, F. ; Groenhof, G.   & Grubmüller, H. ​ (2011) 
    Journal of Chemical Theory and Computation7(6) pp. 1962​-1978​.​ DOI: https://doi.org/10.1021/ct200061r 
    Details  DOI  PMID  PMC 
  • 2011 Journal Article
    ​ ​Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS​
    Kutzner, C.; Czub, J. & Grubmüller, H. ​ (2011) 
    Journal of Chemical Theory and Computation7(5) pp. 1381​-1393​.​ DOI: https://doi.org/10.1021/ct100666v 
    Details  DOI  PMID  PMC 
  • 2010 Journal Article
    ​ ​g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates​
    Hub, J. S. ; de Groot, B. L.   & van der Spoel, D.​ (2010) 
    Journal of Chemical Theory and Computation6(12) pp. 3713​-3720​.​ DOI: https://doi.org/10.1021/ct100494z 
    Details  DOI 
  • 2009 Journal Article
    ​ ​A simple one-body approach to the calculation of the first electronic absorption band of water​
    Mata, R. A. ; Stoll, H. & Cabral, B. J. C.​ (2009) 
    Journal of Chemical Theory and Computation5(7) pp. 1829​-1837​.​ DOI: https://doi.org/10.1021/ct9001653 
    Details  DOI 
  • 2008 Journal Article | Research Paper
    ​ ​United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials​
    Emperador, A.; Meyer, T.   & Orozco, M.​ (2008) 
    Journal of Chemical Theory and Computation4(12) pp. 2001​-2010​.​ DOI: https://doi.org/10.1021/ct8003832 
    Details  DOI  PMID  PMC 
  • 2006 Journal Article
    ​ ​How well can coarse-grained models of real polymers describe their structure? The case of polybutadiene​
    Yelash, L.; Mueller, M.; Paul, W. & Binder, K.​ (2006) 
    Journal of Chemical Theory and Computation2(3) pp. 588​-597​.​ DOI: https://doi.org/10.1021/ct0502099 
    Details  DOI  PMID  PMC  WoS 

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