The hand torsion term is of the Inclusion type (i.e., indexed by the Atom Inclusion Type) and an individual term is: Kt[ tijkl - to ]2 where tijkl is the torsion angle spanned by the atoms i, j, k and l, Kt is the force constant and to is the equilibrium torsion angle. The force constant is assigned to this particular improper torsion angle based on the Atom Inclusion Types of the four participating atoms. The equilibrium angle is set individually for each interation. The Hand module is located in the Energy sub-directory of the Yup package, hence: Yup.Energy.Hand. The hand torsion term is introduced into a simulation by first creating an (empty) instance of the Hand object. Participating atom groups of four atoms are then added to this object, along with the equilibrium torsion angle in degrees. Previously added torsions may also be deleted or modified. All these actions affect only a list of candidate hand torsions. The compile process binds Coordinate and Gradient AtomVectors to the Hand module and then goes through the candidate torsions to form a compiled improper torsion list in which all the atoms that are involved and the improper torsion parameters that they are to use are positively identified. Only then can the improper torsion 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 torsion list is fixed because the Coordinates are different at each call. However, it is possible to modify the force constant continuously during a calculation. The parameters are accessed through the subscript operator. More radical changes can be made by adding new improper torsions and modifying or deleting existing torsions. These actions affect the candidate list and immediately clear the compiled list. Therefore the Hand module must be compiled again before evaluation can resume. The state of the Hand module can be judged by examining the data attributes. The compiled torsions can also be examined in great detail by printing the object. This manual is divided into several pages: Name Content Hand Introduction: this page. Create Creating a new Hand object. The function Hand(). Data The data attributes of a Hand object; some of which may be assigned new values. Manage Managing hand torsions: add new torsions, modifying existing hand torsions and deleting existing torsions. The methods: add(), modify() and delete(). Compile Preparing a Hand object for evaluation of the energy and gradients. The methods: update() and compile(). Evaluate Evaluate the hand torsion energy and gradients. The method: evaluate(). Subscript The subscript [] operator: used to access and to assign values to the hand torsion force constants Print Documents the print, repr, delete and compare operators. Write Writing the finalized hand torsion record to the force field file. Hand 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