Molecular Dynamics Simulations of a Protein in Water and in Vacuum to Study the Solvent Effect

Abstract

Molecular dynamics simulation shows the motions of distinct molecules in models of liquids, solids, and gases. The motion of a molecule defines how its positions, velocities, and orientations change with time. In this study, an attempt has been made to study the solvent effect on the dynamics of Major Prion protein. By keeping the focus mainly on united motions of the molecule, molecular dynamics simulations of Major Prion protein in vacuum and water are performed up to 100 ps. The results obtained from these two simulations are compared to study the solvent effect on the dynamics of Major Prion protein. Energy minimization and molecular dynamics simulation have been done through GROMACS using OPLS-AA force field.