The Hookean bond term is of the Inclusion type (i.e., indexed by the Atom Inclusion Type) and an individual term is: Kb[ rij - bo ]2 where rij is the distance between atoms i and j, Kb is the stretching constant and bo is the equilibrium bond length. The stretching constants are assigned to this particular bond based on the Atom Inclusion Types of the two participating atoms. The equilibrium bond length is specified individually for each term, thus distinguishing this from the very similar Bonds term. This term can be used to implement a coarse-grained model of large molecules, by representing large groups of atoms with a pseudoatom each, and connecting any two pseudoatoms that are within a cutoff distance with this term, thus modeling the molecules with a network of bonds. (This idea comes from the Gaussian Network Model, which uses a coarse-grained normal mode analysis. We are avoiding this name to prevent confusion.) The Hooke module is located in the Energy sub-directory of the Yup package, hence: Yup.Energy.Hooke. The hookean bond term is introduced into a simulation by first creating an (empty) instance of the Hooke object. Participating atom pairs are then added to this object. Previously added bonds may also be deleted or modified. All these actions affect only a list of candidate bonds. The compile process binds Coordinate and Gradient AtomVectors to the Hooke module and then goes through the candidate bonds to form a compiled bond list in which all the atoms that are involved and the bond parameters that they are to use are positively identified. Only then can the bond term be evaluated. (Prior attempts at evaluation will either yield an exception or null results.) The evaluate method would now be called many times as part of a molecular mechanics calculation. Each call would yield different results even though the compiled bond list is fixed because the Coordinates are different at each call. However, it is possible to modify the force constants continuously during a calculation. The parameters are accessed through the subscript operator. More radical changes can be made by adding new bonds and modifying or deleting existing bonds. These actions affect the candidate list and immediately clear the compiled list. Therefore the Hooke module must be compiled again before evaluation can resume. The state of the Hooke module can be judged by examining the data attributes. The compiled bonds can also be examined in great detail by printing the object. This manual is divided into several pages: Name Content Hooke Introduction: this page. Create Creating a new Hooke object. The function Hooke(). Data The data attributes of a Hooke object; some of which may be assigned new values. Manage Managing bonds: add new bonds, modifying existing bonds and deleting existing bonds. The methods: add(), modify() and delete(). Also, the method freeze() that is unique to this term. Compile Preparing a Hooke object for evaluation of the energy and gradients. The methods: update() and compile(). Evaluate Evaluate the bond energy and gradients. The method: evaluate(). Subscript The subscript [] operator: used to access and to assign values to the table of force constants Print Documents the print, repr, delete and compare operators. Write Writing the finalized bond record to the force field file. Yup.Models.Null.HookeFFA is a helper module to generate the terms of this functions. Hooke Create Data Manage Compile Evaluate Subscript Print Write OVERVIEW Bonds Angles Torsions SoftSphereI ElectroI VanderWaalsI DistNOE TorsionSeries GenLJI Potential Hooke Hand Impropers SoftSphereX ElectroX VanderWaalsX SwissCheeseX AngNOE GenLJX