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Simulating Biomolecules with the Variable Protonation State: A Tutorial for Constant-pH Molecular Dynamics in NAMD
Sarah Moe1, Brian K Radak2, Christophe Chipot2,3,4
1Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.
Abstract:
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.
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