next up previous contents index
Next: Overview and Theoretical Background Up: NAMD 2.14b1 User's Guide Previous: Running SMOG simulations   Contents   Index


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.



Subsections

http://www.ks.uiuc.edu/Research/namd/