|
The
energy of the hookean bond between atoms i and j, Eb-ij
is given by:
Eb-ij
= Kb-ij[ bij
- bo-ij ]2
where b
is the distance between atoms i and j, Kb
is the force constant and b0 is the equilibrium
length of the bond. The equilibrium bond length is specified
individually for each and every bond.
The Hooke
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 Hooke
record has the following format:
|
:HOOKE
|
|
:Typei:Typej:
|
Kb-ij
|
|
:Typei:Typej:
|
Kb-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 one number. The names are written between pairs of
colons; the colons are not part of the names. The last number is the
force constant in units of kcal/mol/Å2. Following this
may be text to serve as comment. The comment must be separated, by
white space, from the second number.
A hooke
force constant defined for Inclusion Atom Types :A:B: will
serve equally well for a hooke bond of Types :B:A:. Only the
first instance of a definition of a hooke type will be saved.
Subsequent definitions for the same hooke 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 to form the data table. The
index and data tables are written to the unformatted file: "Hooke
Constants".
|