Effects of system net charge and electrostatic truncation on all‐atom constant pH molecular dynamics

Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all‐atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force‐shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt‐bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini‐protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK_a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation‐state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge‐compensating background plasma. © 2014 Wiley Periodicals, Inc.