|
This
Soft Sphere term is of the Exclusion type (i.e.,
indexed by the Atom Exclusion Type). An Inclusion
version of this term is also available, see
[SoftSphereI]. An individual term
is:
|
{
|
Ks(
rij
-
do
)n
|
, if
rij
<
do
|
|
0
|
, if
rij
>=
do
|
where
rij is the distance between atoms
i and j, Ks is a
force constant, do is the contact
distance and n is a user-specified power. In
contrast to the van der Waals term, the Soft Sphere
term has no attractive component and the repulsion
component operates only when two atoms are closer
together than their contact distance. The repulsion
component is also much softer than in the van der
Waals term although the user may adjust the
softness by specifying larger values of n.
This is a single value specified for the whole
module (and therefore applied equally to all
pairs). It must be a whole number and the value
must be at least 2.
The
SoftSphereX
module is located in the Energy sub-directory of
the Yup package, hence:
Yup.Energy.SoftSphereX.
The
soft sphere term is introduced into a simulation by
first creating an (empty) instance of the
SoftSphereX
object. As this is an Exclusion list term, an empty
object means that all pair interactions will be
considered. This can be modified by adding atom
pairs, whose interaction should not be considered,
to an exclusion list. Previously excluded pairs may
also be removed, which will restore that pair
interaction. All these actions affect only a list
of candidate pairs. The compile process binds
Coordinate and Gradient
AtomVectors
to the SoftSphereX
module and then goes through the candidate pairs to
form a compiled exclusion list in which all the
atoms that are involved are positively identified.
Only then can the soft sphere term be evaluated.
(Prior attempts at evaluation will either yield an
exception or null results.) The evaluate method
would now be called many times as part of a
molecular mechanics calculation. Each call would
yield different results even though the compiled
exclusion list is fixed because the Coordinates are
different at each call. However, it is possible to
modify the soft sphere parameters
(Ks and do)
continuously during a calculation. The parameters
are accessed through the subscript operator. More
radical changes can be made by excluding new pairs
or restoring previously excluded pairs. These
actions affect the candidate list and immediately
clear the compiled list. Therefore the
SoftSphereX
module must be compiled again before evaluation can
resume. The state of the
SoftSphereX
module can be judged by examining the data
attributes. The compiled pairs can also be examined
in great detail by printing the object.
This
manual is divided into several pages:
|
Name
|
Content
|
|
SoftSphereX
|
Introduction:
this page.
|
|
Create
|
Creating
a new SoftSphereX
object. The function
SoftSphereX().
|
|
Data
|
The
data attributes of a
SoftSphereX
object; some of which may be assigned
new values.
|
|
Manage
|
Managing
soft sphere pairs: excluding pairs, and
restoring excluded pairs. The methods:
exclude()
and include().
|
|
Compile
|
Preparing
a SoftSphereX
object for evaluation of the energy and
gradients. The methods:
update()
and compile().
|
|
Evaluate
|
Evaluate
the soft sphere energy and gradients.
The method:
evaluate().
|
|
Subscript
|
The
subscript []
operator: used to access and to assign
values to the soft sphere
parameters
|
|
Print
|
Documents
the print, repr, delete and compare
operators.
|
|
Write
|
Writing
the finalized soft sphere record to the
force field file.
|
|