Model verification

Before starting the simulation is desirable to verify the correctness of the model. There are a few common things, which usually pay attention.

• Each molecule must be either electrically neutral or carry an integer charge. (The exception is when reduced charges are intentionally used. In this case, they must be multiples of the reduction coefficient).

• All atoms must have a molecular mechanical type. Either automatic procedure should be used to install the missing force field parameters (this is a typical situation when testing many new substances, such as ligands).

• The average gradient should not to be great. Its typical value is about 0.5.

• If we study the equilibrium properties of the model, it must be relaxed first. Even the simplest models require no less than 200 ps time for relaxation.

• Do not forget to make a copy of the model before the simulation.

• Very nasty bug that may arise after the simulation is a changing of the chirality. Fortunately, this is a rare problem. However, it can be if we start the simulation from strongly deformed model.