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Constant-pH Simulations 1

Constant-pH MD in NAMD is based on the scheme first proposed by Stern [105] and later revised and extended by Chen and Roux [19]. A detailed description of the modifications and improvements made in the NAMD implementation has been presented elsewhere by Radak, et al. [88] and this is likely the best comprehensive description of the method, its uses, and its limitations/pitfalls. Herein the goal is to provide a working understanding of how the implementation works and what kinds of data it produces.