Simulating Biomolecules with the Variable Protonation State: A Tutorial for Constant-pH Molecular Dynamics in NAMD
This tutorial examines the application of constant-pH molecular dynamics simulations, a method that addresses the critical problem of modeling systems that can adopt multiple protonation states. While conventional molecular dynamics simulations generally assume fixed protonation states, using a constant-pH technique actively explores dynamic shifts in protonation as the simulation progresses. Once completed, constant-pH simulations can be analyzed to yield titration curves that can be readily compared to experiment.
Authors
- Sarah Moe (ORCID: https://orcid.org/0009-0009-1528-7079)
- Christophe Chipot (ORCID: https://orcid.org/0000-0002-9122-1698)
- Brian K. Radak (ORCID: https://orcid.org/0000-0001-8628-5972)
- Benoı̂t Roux (ORCID: https://orcid.org/0000-0002-5254-2712)
Institutions
- University of Illinois Urbana-Champaign (US)
- University of Chicago (US)
- Centre National pour la Recherche Scientifique et Technique (CNRST) (MA)
- Institute of Theoretical Physics (CN)
- Université de Lorraine (FR)
Publication Details
- Journal
- The Journal of Physical Chemistry B
- Published
- 2025-08-04
- DOI
- https://doi.org/10.1021/acs.jpcb.5c03069
- Citations
- 4
- Primary Topic
- Protein Structure and Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 3.22
Funders
- National Institute of General Medical Sciences
- Division of Molecular and Cellular Biosciences