Protein simulations combining an all-atom force field with a Go term

Abstract

Using a variant of parallel tempering, we study the changes in sampling within a simulation when the all-atom model is coupled to a Go-like potential. We find that the native structure is not the lowest-energy configuration in the all-atom force field. Adding a Go-term deforms the energy landscape in a way that the native configuration becomes the global minimum.

9 pages, 8 figures