Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics. - Oliver F. Lange; Lars V. Schäfer; Helmut Grubmüller (J. Comput. Chem., 2006)

Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595. - Lars V. Schäfer; Gerrit Groenhof; Martial Boggio-Pasqua; Michael A. Robb; Helmut Grubmüller (PLoS Comput. Biol., 2008)

Reconstruction of atomistic details from coarse-grained structures. - Andrzej J. Rzepiela; Lars V. Schäfer; Nicolae Goga; H. Jelger Risselada; Alex H. de Vries; Siewert J. Marrink (J. Comput. Chem., 2010)

Polarizable Water Model for the Coarse-Grained MARTINI Force Field. - Semen O. Yesylevskyy; Lars V. Schäfer; Durba Sengupta; Siewert J. Marrink (PLoS Comput. Biol., 2010)

Determining equilibrium constants for dimerization reactions from molecular dynamics simulations. - Djurre H. De Jong; Lars V. Schäfer; Alex H. de Vries; Siewert J. Marrink; Herman J. C. Berendsen; Helmut Grubmüller (J. Comput. Chem., 2011)

Viscosity Prediction of High-Concentration Antibody Solutions with Atomistic Simulations. - Tobias M. Prass; Patrick Garidel; Michaela Blech; Lars V. Schäfer (J. Chem. Inf. Model., 2023)

Optimized Protein-Excipient Interactions in the Martini 3 Force Field. - Tobias M. Prass; Kresten Lindorff-Larsen; Patrick Garidel; Michaela Blech; Lars V. Schäfer (J. Chem. Inf. Model., 2025)