Molecular Simulations

The objective of my work is to find the free energy of the protein system and to utilize it so as to find various other properties of protein and/or protein-ligand complex. The method used to find free energy is the thermodynamic integration method in which the Hamiltonian is made dependent of a coupling parameter λ representative of the state of the system. The simulations were performed on the software GROMACS and the results were used in finding the free energy of the system.The free energy data were then used to find the solvation energy of a ligand named B-Octylglucoside (BOG). The free energy calculations were also used to find the binding energy of the ligand BOG attached to the monomeric outer-membrane porin OmpG (a protein-ligand complex).

Molecular simulations, mainly using the Molecular Dynamics (MD) and Monte Carlo (MC) techniques, are used in physics, chemistry, and several more applied sciences to link the properties of individual molecules (which can be assessed e.g. by quantum mechanical methods) with the properties (observables at given thermodynamics conditions, e.g. temperature and/or pressure) of macroscopic systems consisting of these molecules. Only such simulations allow for a description of the molecular properties sophisticated enough to catch the specificities of many real systems that may be of chemical or physical interest. It is an additional strength of these methods that several observables can be obtained in a consistent way from a single molecular description (model). A few examples of what can be done with this approach and of how it is embedded in other theoretical description of matter are discussed.

This introductory chapter traces the development of the molecular theory of fluids as it has evolved over roughly the last 200 years. Many of the modern variations of molecular theory applied to fluids originated in the last quarter of the 1800s with the contributions of van der Waals; this chapter is organized to reflect that fact. The overview of present day techniques presented here includes brief discussions of theoretical, experimental, and computer simulation methods. The intent is to provide some historical perspective for the remainder of this volume.