Protonation states of biologically relevant molecules (proteins, lipids, etc.) are fundamental for their function and are influenced by pH and electrostatic interactions with neighboring molecules. Accurately capturing protonation shifts with molecular dynamics (MD) may considerably improve the understanding of pH-dependent processes [1<https://doi.org/10.1101/2024.11.27.625717>, 2<https://doi.org/10.1101/2024.12.06.627182>]. However, classical MD employs fixed protonation states impeding dynamical modeling of protonation changes.

This two-day advanced course introduces a recent extension of the GROMACS engine that enables constant-pH molecular dynamics (cpHMD) using λ-dynamics [3<https://doi.org/10.1021/acs.jctc.2c00516>]. Participants will learn how to prepare, run, and analyze cpHMD simulations of a soluble protein, including trajectory post-processing. This is an advanced course; intermediate knowledge of GROMACS and the Linux environment is required.

The course is offered in person at the Department of Biology at Friedrich-Alexander-Universität Erlangen-Nürnberg and is limited to eight participants. Interested candidates should send a short note about their background and motivation to rainer.boeckmann@fau.de (Deadline: 20. March 2026). There are options for travel grants for participants. We welcome applicants of all backgrounds and especially encourage those from underrepresented groups in the natural science to apply.