Comparison of implicit solvent models and force fields in molecular dynamics simulations of the PB1 domain

Abstract

The dynamics of the Phox and Bem1p (PB1) domain, which adopts an ubiquitin-like β-grasp fold, have been simulated using two implicit solvent models (GBSW and EEF1.1) and two force fields (CHARMM19 and 22). The protein undergoes a large re-orientation using EEF1.1 with the CHARMM19 force field. This computational model is often applied in folding simulations. However, the conformational dynamics generated using EEF1.1 with the CHARMM22 force field are similar to those in the GBSW simulations and do not show any large re-orientation. These findings underscore the care needed in the selection of, not only the implicit solvent model, but also an appropriate protein force field.