The van der Waals (more accurately, the Lennard-Jones) term comes in two versions, an inclusion list version (this version vdw+) and an exclusion list version (see vdw- next). In the inclusion list version, the pairs of atoms that contribute to this interaction are explicitly listed. In the exclusion list version, every pair of atoms in the system is assumed to contribute to the total van der Waals interaction unless explicitly excluded in an exclusion list. The inclusion list version is the correct choice if there is only a small number of interactions; the vdw- term will require a prohibitively large exclusion list. The vdw- term is a better choice if the majority of atom pairs contribute to the van der Waals interaction; the vdw+ term would have required a very long listing of pairs. Only one version or the other should be used in a descriptor; it is unlikely to be useful (but it is not impossible) to use both versions in a single descriptor.

The vdw+ energy is the sum of N_vdw terms each of the form:

T[ rij ]{ A / rij12 - B / rij6 }

where T[ r_ij ] is a trimming function, which operates from zero or r_start and completes its transformation at r_finish. Trimming Function Details [will open in a separate window]. A and B are constants dependent on the atoms atom_i and atom_j and r_ij is the current distance between these two atoms.

The vdw+ record in the descriptor file has the form:

vdw+	trim	Nvdw	rstart	rfinish	rcutoff
	atomi	atomj	A	B
	...	...	...	...

The record starts with the keyword vdw+ followed by a code trim, then the number of atom pairs N_vdw, the starting distance at which the trimming starts r_start, the distance at which trimming is complete r_finish and finally the cutoff distance r_cutoff. The last is not used in this calculation but is required anyway.

Following the header line are N_vdw lists each list containing four numbers: the atom pair atom_i and atom_j and the constants A and B.

trim is a code to select the trimming function as follows:

trim	1	2	3
Trimming Function	Truncate	Switch	Shift

Trmming modifies the van der Waals function. To minimize the effect, select the truncation function (trim = 1) and set a very large value for r_finish (the largest linear dimension of the system for example). Note that this version of the van der Waals term is not designed for large lists; every pair of atoms that is listed in this record is evaluated regardless of their distance from one another. Selecting the Truncation triming function and a large value for r_finish will not increase memory usage and will only slightly increase the number of computations.

Example:

vdw+   2   5   12.5   15.0   15.0

1    7   107780   5041
1    8   107800   5060
1   11   120650   6885
2    7   107800   5060
2   11    12840   1859

A vdw+ record with 5 terms. The Switching function is selected and it will operate from 12.5Å to 15Å.