Hydrodynamic parameters of hydrated macromolecules: Monte Carlo calculation

Abstract

A theoretical model for computing the basic hydrodynamic parameters of macromolecules in a water environment is presented. Starting from the 3D structure of the molecule, taking into account the hydration shell, the following parameters are calculated: translation friction coefficient, diffusion coefficient and intrinsic viscosity. The novel Monte Carlo algorithms also work effectively in the case of large molecules. The consumption of CPU time is proportional to N^q, where N is the number of atoms in the molecule and q a coefficient of 1.6–1.7, respectively.