Tomáš Trnka

ReaxFF Parameter Optimization with Monte-Carlo and Evolutionary Algorithms: Guidelines and Insights

Ganna Shchygol, Alexei Yakovlev, Tomáš Trnka et al. · Journal of Chemical Theory and Computation · 2019 · 79 citations · Full text

Engineering, Error Reaxff, Evolutionary Algorithms +19

The Amsterdam Modeling Suite

Evert Jan Baerends, Néstor F. Aguirre, N. Austin et al. · The Journal of Chemical Physics · 2025 · 63 citations · Full text

Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions

Tomáš Trnka, Igor Tvaroška, Jaroslav Koča · Journal of Chemical Theory and Computation · 2017 · 39 citations

Engineering, Molecular Biology, Computational Chemistry +23

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

Tomáš Trnka, Stanislav Kozmon, Igor Tvaroška et al. · PLoS Computational Biology · 2015 · 27 citations · Full text

Potential Energy Surface, Glycobiology, Molecular Biology +16

Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2

Pavel Janoš, Tomáš Trnka, Stanislav Kozmon et al. · Journal of Chemical Theory and Computation · 2016 · 15 citations

Bioorganic Chemistry, Engineering, Molecular Biology +18