Theoretical Approaches for Multiscale Computer Simulations

Abstract

This chapter presents a summary of main theoretical methods that are implemented in MBN Explorer. The significant part of the methodologies outlined is devoted to the classical molecular dynamics, which is based on the concept of molecular force fields. A variety of different force fields is introduced and their applicability to the description of molecular systems of different kind is discussed. Special attention is paid to biomolecular systems. The key algorithms (integrators, linked cell approach, Ewald summation, etc.), as well the essential aspects of the computational realisation of molecular dynamics (thermostats, boundary conditions, etc.) are elaborated in details. The basic ideas towards the multiscale description of MBN systems by means of kinetic Monte Carlo approach and the irradiation driven molecular dynamics are introduced and discussed.