Introducing titratable water to all-atom molecular dynamics at constant pH

Citations of this article
Mendeley users who have this article in their library.


Recent development of titratable coions has paved the way for realizing all-atom molecular dynamics at constant pH. To further improve physical realism, here we describe a technique in which proton titration of the solute is directly coupled to the interconversion between water and hydroxide or hydronium. We test the new method in replica-exchange continuous constant pH molecular dynamics simulations of three proteins, HP36, BBL, and HEWL. The calculated pKa values based on 10-ns sampling per replica have the average absolute and root-mean-square errors of 0.7 and 0.9 pH units, respectively. Introducing titratable water in molecular dynamics offers a means to model proton exchange between solute and solvent, thus opening a door to gaining new insights into the intricate details of biological phenomena involving proton translocation. © 2013 Biophysical Society.




Chen, W., Wallace, J. A., Yue, Z., & Shen, J. K. (2013). Introducing titratable water to all-atom molecular dynamics at constant pH. Biophysical Journal, 105(4).

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free