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The
energy of the soft sphere contact between atoms
i and j, Ess-i,j
is:
Ess-ij
= Kss-ij[
dij -
do-ij
]n,
dij <
do-ij
and
is zero for other distances. d is the
distance between the atoms, Kss
is the force constant and d0 is
the contact distance. n is a variable power
(should be even) that is specified during run time.
This force term is available in two variants:
Inclusion and Exclusion (described
here).
The
Soft Sphere Exclusion record must appear
only after the Atom Exclusion Types have
been defined. The Soft Sphere Exclusion
record has the following format:
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:SOFT-SPHERE-EXCLUSION
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Kss-1,1
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Kss-1,2
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Kss-1,3
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...
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...
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Kss-N-1,N-1
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Kss-N-1,N
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Kss-N,N
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d0-1,1
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d0-1,2
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d0-1,3
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...
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...
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d0-N-1,N-1
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d0-N-1,N
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d0-N,N
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.END
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The
opening keyword, like all keywords, begins with a
colon and starts on column one of the line. There
is no terminating keyword but it is not a bad idea
to close the record with a word that looks like the
termination keyword, for example ".END". If there
are N
Atom Exclusion Types, then
N(N+1)/2
force constants in units of
kcal/mol/Ån must follow the
opening keyword. This must then be followed by the
same number of contact distances in units of
Å. The numbers must be written in proper
order, with the second index varying fastest. Any
number of numbers may be placed on each line
subject to the maximum width of a line of 1023
characters. There is no way to insert comments
among the numbers.
The
mixing rules used to calculate the constants for
mixed-pairs from values for pure-pairs should be
documented in the source file.
The
program Yup.fpf
will convert the force constants to internal units
used by YUP
and write these and the contact distances to the
unformatted file: "Soft
Sphere Exclusion
Constants".
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