ABSTRACT
In this chapter I outline the general principles of modeling biomacromolecules with internal coordinates as independent variables. This approach was generally preferred in the early period of computer conformational analysis when hardware computer resources were strongly limited [1]. In the last two decades, mainly because of the growing interest in molecular dynamics (MD), Cartesian coordinate approaches gradually became predominant, and one readily sees that just by looking into the index of this book. Nevertheless, internal coordinates continue to be employed, notably, in conformational searches based on energy minimization and Monte Carlo (MC) [2] and in normal mode analysis [3]. My main objective is to give a consistent exposition of the basic algorithms of this methodology and its underlying philosophy, with special emphasis on recent advances in the internal coordinate molecular dynamics (ICMD) techniques.
