AUTHOR=Joerg Florian , Wieder Marcus , Schröder Christian 

TITLE=Protex—A Python utility for proton exchange in molecular dynamics simulations

JOURNAL=Frontiers in Chemistry

VOLUME=11

YEAR=2023

URL=https://www.frontiersin.org/journals/chemistry/articles/10.3389/fchem.2023.1140896

DOI=10.3389/fchem.2023.1140896

ISSN=2296-2646

ABSTRACT=<p><monospace>Protex</monospace> is an open-source program that enables proton exchanges of solvent molecules during molecular dynamics simulations. While conventional molecular dynamics simulations do not allow for bond breaking or formation, <monospace>protex</monospace> offers an easy-to-use interface to augment these simulations and define multiple proton sites for (de-)protonation using a single topology approach with two different <italic>λ</italic>-states. <monospace>Protex</monospace> was successfully applied to a protic ionic liquid system, where each molecule is prone to (de-)protonation. Transport properties were calculated and compared to experimental values and simulations without proton exchange.</p>