Preparation of an MD Simulation

The following steps contain the build-up of the molecular topology and the choice of the convenient general simulation conditions. 

The general setup of an MD run comprehends the system size (dimensions of the simulation box), the temperature and the pressure which affect the molecule(s) and the treatment of the system boundaries. In almost all cases it is recommended to simulate with periodic boundary conditions in order to avoid unwanted surface effects due to the artificial box walls. Periodic boundary conditions are implemented in such a way that the box is completely encircled by identical copies of itself [140, 141]. 

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