CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations.

ABSTRACT: Coarse-grained (CG) and multiscale simulations are widely used to study large biological systems. However, preparing the simulation system is time-consuming when the system has multiple components, because each component must be arranged carefully as in protein/micelle or protein/bilayer systems. We have developed CHARMM-GUI PACE CG Builder for building solution, micelle, and bilayer systems using the PACE force field, a united-atom (UA) model for proteins, and the Martini CG force field for water, ions, and lipids. The robustness of PACE CG Builder is validated by simulations of various systems in solution (α3D, fibronectin, and lysozyme), micelles (Pf1, DAP12-NKG2C, OmpA, and DHPC-only micelle), and bilayers (GpA, OmpA, VDAC, MscL, OmpF, and lipid-only bilayers for six lipids). The micel

SUBMITTER: Qi Y 

PROVIDER: S-EPMC3985889 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature