Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations. - Noah S. Bieler; Tuomas P. J. Knowles; Daan Frenkel; Robert Vácha (PLoS Comput. Biol., 2012)

Selecting Collective Variables and Free-Energy Methods for Peptide Translocation across Membranes. - Ivo Kabelka; Radim Brozek; Robert Vácha (J. Chem. Inf. Model., 2021)

Split Membrane: A New Model to Accelerate All-Atom MD Simulation of Phospholipid Bilayers. - Mehrnoosh Khodam Hazrati; Lukás Sukeník; Robert Vácha (J. Chem. Inf. Model., 2025)

Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations. - Timothée Rivel; Denys Biriukov; Ivo Kabelka; Robert Vácha (J. Chem. Inf. Model., 2025)

Role of Divalent Ions in Membrane Models of Polymyxin-Sensitive and Resistant Gram-Negative Bacteria. - Mariia Savenko; Robert Vácha; Christophe Ramseyer; Timothée Rivel (J. Chem. Inf. Model., 2025)

gorder: Comprehensive tool for calculating lipid order parameters from molecular simulations. - Ladislav Bartos; Peter Pajtinka; Robert Vácha (SoftwareX, 2025)