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Atom
Inclusion Groups are collections of Atom
Inclusion Types that are used to define
force-field terms for combinations of Atom
Inclusion Types. (Groups are very similar to
wildcards.) Atom Inclusion Groups are used
only in the definition of force-field terms.
Groups are expanded into their members and
the expanded data is written to the output files.
Atom Inclusion Groups do not exist outside
the source file.
The
Atom Inclusion Group record must appear only
after the Atom Inclusion Type record has
been defined. The format of the Atom Inclusion
Group record is:
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:ATOM-INCLUSION-GROUP
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:Name1:Member1:Member2:...:
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:Name2:Member1:Member2:...:
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...
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:END
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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 names. The names are written
between pairs of colons; the colons are not part of
the names. Following the closing colon may be text
to serve as comment. The comment must be separated
from the name by white space, and may not contain
colons.
The
first name of each list is the name of the Atom
Inclusion Group. This must not be the same as
an existing Atom Inclusion Type. The other
names that follow must be names of Atom
Inclusion Types declared earlier; these are the
members of the group. If a group contains too many
members to be listed in a single line, start new
lines beginning with the Group name and list
more members in each line. It is an error to add a
member to a Group more than once.
Groups are independent of one another; an
Atom Inclusion Type may belong to more than
one Group. It is a good idea to give
distinctive names to Groups so that they
stand out from names of Types. For example,
use brackets, parentheses, braces, angle brackets
and so on.
Atom
Inclusion Groups are of greatest use in
torsions and improper torsions where data is
available only for a limited number of combinations
of Atom Inclusion Types. There may be a
temptation to define a Group that encompass
all Atom Inclusion Types and use it in
defining proper and improper torsion parameters.
This is not a good idea because each combination
that arises from the expansion of the Group
is added to the index table of the proper and
improper torsion output files, and large
Groups lead to even larger combinations. It
is much better to define smaller Groups that
are more specific. This has the added advantage
that illogical connections will be
caught.
Groups
may be used in bond and angle terms but effort
should be directed towards minimizing the number of
Types in the first place.
When
defining the parameters for a force field term,
bear in mind that only the first definition for a
particular grouping of Types is saved.
Subsequent definitions for the same grouping are
silently ignored. Thus, definitions that use
Groups should be placed at the end of the
list so that the generic definitions do not
override the more specific definition.
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