Computer Simulation of Met-Enkephalin Using Explicit Atom and United Atom Potentials: Similarities, Differences, and Suggestions for Improvement

摘要

The conformational dynamics of Met-enkephalin are studied using a variety of united atom and explicit atom force fields to compare and contrast the dynamical behavior predicted by these two types of force fields in biological systems. Equilibrium and dynamical properties are computed from 130-ns implicit water, Langevin dynamics (LD) simulations for four explicit atom and two united atom force fields. The dynamical properties discussed provide a reasonable probe of conformational regions not covered by equilibrium folded structures and are very useful in testing and improving force fields. A comparison of these dynamical properties indicates that the explicit atom and united atom force fields produce significantly different peptide dynamical properties.