All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

ABSTRACT: Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HE

SUBMITTER: Huang Y 

PROVIDER: S-EPMC5713900 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature