OPEP6: A new constant-pH Molecular Dynamics simulation scheme with OPEP coarse-grained force field

The great importance of pH for molecular processes has motivated the continuous development of numerical methods to improve the physical description of molecular mechanisms in computer simulations. Although rigid titration models are able to provide several pieces of useful information, the coupling between the molecular conformational changes and the acid–base equilibrium is necessary to more completely model the pH effects in biomolecules. Previously reported convergence issues with atomistic simulations indicated that a promising approach would require coarse-grained models. By means of the coupling between the successful OPEP force field for proteins with the fast proton titration scheme, we proposed a new protocol for constant-pH molecular dynamics simulations that takes advantage of both coarse-grained approaches to circumvent sampling difficulties faced by other numerical schemes and also to be able to properly describe electrostatic and structural properties at lower CPU costs. Here, we introduce ...