This van der Waals term is of the Exclusion type (i.e., indexed by the Atom Exclusion Type). An Inclusion version of this term is also available, see [VanderWaalsI]. An individual term is: A12 - B6 rij12 rij6 where rij is the distance between atoms i and j, A12 and B6 are force constants. The two constants are assigned to this particular pair based on the Atom Exclusion Types of the two participating atoms. The van der Waals term is asymptotic and so there is potentially a very large number of pair interactions to be considered. Usually, only the pairs that are within a limited cutoff distance are considered. This creates a discontinuity at the cutoff point which can be minimized by using a large cutoff distance. The discontinuity can be artifically eliminated by applying a trimming function. This is a piecewise continuous function (below) that is multiplied on the plain van der Waals function (above): 1 , if rij <= rstart ( rfinish - rij )2( rfinish + 2rij - 3rstart ) , if rstart < rij < rfinish ( rfinish - rstart )3 0 , if rij >= rfinish Trimming starts at the distance rstart and at rfinish the value and gradient are both 0. Normally, rstart is set beyond the cutoff distance so the trimming function is not used. In order to apply the trimming function, set rstart to a value less than rfinish that in turn is less than the cutoff distance. Distances are specified as proportions of the van der Waals distance: [ 2A12 / B6 ]1/6 which is different for each pair type. The VanderWaalsX module is located in the Energy sub-directory of the Yup package, hence: Yup.Energy.VanderWaalsX. The van der Waals term is introduced into a simulation by first creating an (empty) instance of the VanderWaalsX object. As this is an Exclusion list term, an empty object means that all pair interactions will be considered. This can be modified by adding atom pairs, whose interaction should not be considered, to an exclusion list. Previously excluded pairs may also be removed, which will restore that pair interaction. All these actions affect only a list of candidate pairs. The compile process binds Coordinate and Gradient AtomVectors to the VanderWaalsX module and then goes through the candidate pairs to form a compiled exclusion list in which all the atoms that are involved are positively identified. Only then can the van der Waals 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 exclusion list is fixed because the Coordinates are different at each call. However, it is possible to modify the van der Waals parameters (A12 and B6) continuously during a calculation. The parameters are accessed through the subscript operator. More radical changes can be made by excluding new pairs or restoring previously excluded pairs. These actions affect the candidate list and immediately clear the compiled list. Therefore the VanderWaalsX module must be compiled again before evaluation can resume. The state of the VanderWaalsX module can be judged by examining the data attributes. The compiled pairs can also be examined in great detail by printing the object. This manual is divided into several pages: Name Content VanderWaalsX Introduction: this page. Create Creating a new VanderWaalsX object. The function VanderWaalsX(). Data The data attributes of a VanderWaalsX object; some of which may be assigned new values. Manage Managing van der Waals pairs: excluding pairs, and restoring excluded pairs. The methods: exclude() and include(). Compile Preparing a VanderWaalsX object for evaluation of the energy and gradients. The methods: update() and compile(). Evaluate Evaluate the van der Waals energy and gradients. The method: evaluate(). Subscript The subscript [] operator: used to access and to assign values to the van der Waals parameters Print Documents the print, repr, delete and compare operators. Write Writing the finalized van der Waals record to the force field file. VanderWaalsX 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