|
The
energy of the van der Waals contact between atoms
i and j, Evdw-ij
is:
|
Evdw-ij
=
|
Avdw-ij
|
-
|
Bvdw-ij
|
|
|
|
rij12
|
rij6
|
where.
rij is the distance between atoms
i and j, Avdw-ij
and Bvdw-ij are force parameters.
This force term is available in two variants:
Inclusion (described here) and
Exclusion.
The
van der Waals Inclusion record must appear
only after the Atom Inclusion Types have
been defined. This record must also appear after
the Atom Inclusion Group record if
Groups are used in this record. The van
der Waals Inclusion record has the following
format:
|
:VAN-DER-WAALS-INCLUSION
|
|
|
:Typei:Typei:
|
Kss-ii
|
d0-ii
|
|
|
:Typei:Typej:
|
Kss-ij
|
d0-ij
|
|
|
...
|
...
|
...
|
|
:END
|
The
opening and closing keywords, like all keywords,
begin with a colon and start on column one of their
respective lines. The body of the data section may
contain any number of lines. A line may be empty or
may contain a list of two Atom Inclusion
Type or Group names followed by two
numbers. The names are written amongst three
colons; the colons are not part of the names. The
first number is the factor for the reciprocal 12
term in units of Å12kcal/mol. The
second number is the factor for the reciprocal 6
term in units of Å6kcal/mol.
Following the second number may be text to serve as
comment. The comment must be separated, by white
space, from the second number.
A
van der Waals type defined for Inclusion Atom
Types :A:B: will serve equally well for a van
der Waals interaction of Types :B:A:. Only
the first instance of a definition of a van der
Waals type will be saved. Subsequent definitions
for the same van der Waals type will be silently
ignored. Therefore, definitions using Groups
should be placed at the end of the list so that the
generic defintions do not override the specific
definitions.
The
program Yup.fpf
will expand Groups into their component
Types, hash each pair of Types into a
numerical code, and sort the codes. This forms the
index table. The force constants are converted to
internal units used by
YUP
and these numbers form the data table. The index
and data tables are written to the unformatted
file: "van
der Waals Inclusion
Constants".
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