Author

Vytautas Gapsys

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Force Fields and Simulation Engines: Lessons Learned from Porting Amber ﬀ14SB and ﬀ19SB to GROMACS

The ported and validated Amber protein force ﬁelds for use with GROMACS reproduce the Amber reference topologies exactly, with per-interaction energies matching to within the single-precision ﬂoating-point limit (< 10 −7 kJ/mol).

Vedran Miletić, Miłosz Wieczór, C. Simmerling et al. · 0 citations

Open access Jul 2026

Benchmarking Docking Protocols on Predicting Alternative Binding Modes

Assessment of pose prediction methods when the bound structure of a reference ligand is known and the likely binding mode(s) of a related compound are needed, and this work focuses on cases where the new compound has multiple potential binding modes.

Ažbeta Kubincová, S. S. Çınaroğlu, Jianna Ongsioco et al. · Journal of Chemical Informat... · 0 citations