There exist several commands which can modify the way the potential energy is calculated or can affect the way energy manipulations are performed.
The CONSTRAINT command, see Constraints, can be used to set constraints of various kinds. First, it can be used to set flags for particular atoms which will prevent them from being moved during minimization or dynamics. Second, it can be used to add positional constraint term to the potential energy. This term will be harmonic about some reference position. The user is free to set the force constant. Third, the user can place a harmonic constraint on the value of particular torsion angles in an attempt to force the geometry of a molecule. Fourth, atoms can be fixed in place. When atoms are fixed, they are not allowed to move at all. Any energy terms involving nothing but fixed atom are ignored, because they will have no effect. In addition the trajectories written by the dynamics command only have one copy of the fixed atom coordinates written. Thus, such trajectories take less disk space.
The SHAKE command, see Shake Command, is used to set constraints on bond lengths and also bond angles during dynamics. It is very valuable in that it permits a larger step size to be used during dynamics. This is vital for dynamics where hydrogens are explicitly represented as the low mass and high force constant of bonds involving hydrogen require a ridiculously small step size.
The WEIGHT command, see Weight Command, is used to change the weights on each of the terms in the potential energy function. This is useful during dynamics with NMR constraints when one is interested in getting to the final solution as quick as possible.
The user interface commands, see CONGEN Modifications, can be used to modify the calculation of the potential and to add another term to the potential energy.