Before the energy of a system can be evaluated and manipulated, a number of data structures must be present.
First, a PSF must be present.
Second, a parameter set must be present. It must contain all parameters which are required by the PSF being used.
Third, coordinates must be defined for every atom in the system. An undefined coordinate has a particular value, and if two coordinates have the same value, division by zero will occur in the evaluation of the energy. If the positions of hydrogens are required, the hydrogen bond generation routine, see HBUILD Command), must be called before the energy is evaluated. In the case of energy evaluations, CONGEN will ignore interactions involving undefined atom positions. However, minimization and dynamics will fail if any positions are unknown.
Fourth, provisions must be made for having a hydrogen bond list and a non-bonded interaction list. Having non-zero frequencies for updating this lists is one way, one can also read these lists in, see Read Command, or generate them with separate commands, see Hydrogen Bonds, or Non-bonded Interactions.
All of these requirements can be met through the use of a restart file, see Dynamics.