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In the
Swiss Cheese term, a collection of holes in space attract any
atoms that are within a given range. The value of the Swiss Cheese term
between an atom p and a hole q, Eswch-pq is
given by:
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Eswch-pq
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={ |
-E0Spq
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if rpq
<= di
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E0[do-rpq]2[3di-2rpq-do]Spq[do-di]-3
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if di < rpq
< do
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0
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if rpq
>= do
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where rpq
is the distance between the atom p
and the hole q, di and do
are the inner and outer radii of the hole, E0 is the depth of the
hole [kcal/mol]. This function is that of a flat-bottomed well, with a
smoothly sloping walls between di and do.
The factor Spq is
given by the following:
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Spq
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={ |
Ap/Oq
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if Ap
< Oq
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Oq/Ap
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if Ap
>= Oq
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where Ap
is a constant assigned according to the exclusion atom type of atom p and Oq is a
constant associated with the hole q.
Both groups of constants are numbers ranging from a small positive
value to a maximum value of 1.0. The constants E0, di, do are set within the SwissCheeseX module. The
coordinates of the center of the holes and the constants O for each hole are read from a
file and stored in the SwissCheeseX module.
The
constants A are specified in
the parameter library. The SwissCheeseX
record must appear only after the Atom Exclusion Types have
been defined. The SwissCheeseX record has the following
format:
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:SWISS-CHEESE-EXCLUSION
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A1
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A2
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...
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.END
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The
opening keyword, like all keywords, begins with a colon and starts on
column one. The body of the data section must contain as many numbers
as the number of exclusion atom types. The constants must be given in
the same order as the exclusion atom types. Numbers must be positive,
never zero,
or exceed the value 1.
The
program Yup.fpf will convert SwissCheeseX
into a table that is written to the unformatted file: "Swiss Cheese
Exclusion Constants".
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