EXTENDED MOLECULAR-DYNAMICS AND OPTIMIZED ROUSE-ZIMM MODEL STUDIES OFA SHORT PEPTIDE - VARIOUS FRICTION APPROXIMATIONS

Developing a theory for the long time dynamics of polypeptides require s not only a proper choice of the relevant dynamic variables, but also a meaningful definition of friction coefficients for the individual a toms or groups of atoms in the reduced system. We test various aspects of the optimized Rouse-Zimm model for describing the long time rotati onal dynamics of a peptide fragment. The necessary equilibrium input i nformation is constructed from a 1 ns molecular dynamics simulation fo r the solvated peptide by using a parallel Gray version of CHARMm, who se new features are described here. The simulations also provide time autocorrelation functions for comparisons with both theoretical predic tions and with experiment. Two atomic friction models (van der Waals r adii and accessible surface area) are chosen, and tests are made of th e applicability of two combining rules for calculating the group frict ion coefficients. While the rotational dynamics of the peptide is inse nsitive to the friction models used, the combining rules are found to impact profoundly upon the theoretical descriptions for the behavior o f the peptide dynamics for the reduced descriptions with fewer variabl es. The calculations study the role of the memory functions, neglected in this dynamical theory, and the interatomic hydrodynamic interactio ns in constructing the group friction coefficients. While the I ns tra jectory is longer than customarily used for very complex systems, ther e are nontrivial influences of the duration of the molecular dynamics trajectory on the description of the dynamics. (C) 1995 American Insti tute of Physics.