Minimization and Molecular Dynamics
For refinement of the receptor model on the one hand and to analyze conformational changes of the receptor on time scale on the other hand, in general molecular dynamic simulations of the receptor in its natural environment are performed. As a first step the so called setup of the simulation box is explained in detail and deals with the construction of the ligand, the receptor and the surrounding membrane. As the next step the embedding of the ligand-receptor complex into the membrane is elaborated with the help of appropriate LINUX commands. Finally different simulation protocols splitting the molecular dynamic procedure into a equilibration and a productive phase are presented.