ABSTRACT
This chapter focuses on systematic coarse-graining methodology based on the Inverse Monte Carlo (IMC) method. It discusses the term "IMC" only in application to multiscale coarse-graining, while there exists a more general definition of "IMC" as a solution of any inverse problem by any type of Monte Carlo (MC) technique Dunn and Shultis. The IMC method is currently implemented in two open source software packages: versatile object-oriented toolkit for coarse-graining applications (VOTCA) Rühle et al and Magic Mirzoev and Lyubartsev. The Magic package was developed specially to implement systematic structure-based coarse-graining of arbitrary molecular models using the IMC or iterative Boltzmann inversion (IBI) methodology. The chapter considers various applications of IMC methodology to ionic systems, lipid assemblies, Deoxyribo Nucleic Acid (DNA), and few other systems. It looks at theoretical background, practical algorithms, problems, and possible limitations of the approach. The Newton inversion algorithm can be straightforwardly implemented if number of potential parameters is equal to the number of target properties.
