Extending GROMACS/pmx from mutations to protein covalent chemistry
A webinar by the BioExcel Center of Excellence for Computational Biomolecular Research will present their past and present work extending alchemical free-energy calculations in GROMACS/pmx to quantify the thermodynamic consequences of these changes. The webinar will be held on 13 October 2026.
Many biological processes are regulated by changes in protein covalent chemistry, from protonation and disulfide formation to post-translational modification. In this webinar, BioExcel will present their past and present work extending alchemical free-energy calculations in GROMACS/pmx to quantify the thermodynamic consequences of these changes. After a brief introduction to free-energy methods, they will discuss the ongoing work toward a general framework for covalent protein modifications and highlight some applications to biological questions, including pH-dependent gating of aquaporins and modification-driven changes in amyloid fibril stability.