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The 14
existing and 7 future Energy
modules implement the individual terms of the potential energy
function. These terms quantify the interaction of groups of one to four
atoms. Some terms are available in two versions: an Inclusion or an
Exclusion version. Inclusion terms assume no interactions except those
that are explicitly added to the term. Exclusion terms assume that all
pair interactions are considered, except for those pairs that are
explicitly excluded.
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MODULE
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POTENTIAL ENERGY TERM
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EnergyID |
[1]
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[2]
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[3]
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[4]
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Bonds
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Bond
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100001 |
2
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N
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B
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E
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Morse
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100002 |
2
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N
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B
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E
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Angles
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Angle
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100003 |
3
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N
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B
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E
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Angle Power Series
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100004 |
3
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N
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B
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E
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Torsions
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Torsion
(Cosine Series)
|
100005 |
4
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N
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B
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E
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Impropers
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Improper
Torsion
|
100007 |
4
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N
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B
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E
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Torsion Power Series
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100006 |
4
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N
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B
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E
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SoftSphereI
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Soft
Sphere Inclusion
|
100009 |
2
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N
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U
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E
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SoftSphereX
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Soft
Sphere Exclusion
|
100008 |
2
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X
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U
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E
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ElectroI
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Electrostatics
Inclusion
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100013 |
2
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N
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U
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E
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ElectroX
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Electrostatics
Exclusion
|
100012 |
2
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X
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U
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E
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VanderWaalsI
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van
der Waals Inclusion
|
100011 |
2
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N
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U
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E
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VanderWaalsX
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van
der Waals Exclusion
|
100010 |
2
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X
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U
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E
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Generalized Lennard-Jones
Inclusion
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100015 |
2
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N
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U
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E
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Generalized Lennard-Jones
Exclusion
|
100014 |
2
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X
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U
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E
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Noens
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Distance
NOE
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100016 |
2
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N
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UB
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C
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| Hooke |
Hookean Bond Network |
100019 |
2 |
N |
B |
E |
| Hand |
Chiral constraints for a
Network |
100022 |
4 |
N |
B |
C |
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Angle NOE
|
100017 |
3
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N
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UB
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C
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SwissCheeseX
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Swiss Cheese
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100020 |
1
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X
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U
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C
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Stud
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100018 |
1
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N
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B
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C
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The
explanations for the numbered columns are:
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#
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DESCRIPTION
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[1]
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Number
of interacting atoms per term
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[2]
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Inclusion
(N) or Exclusion (X) term.
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[3]
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Interaction
amongst closely bonded (B) or non-bonded or unrelated atoms (U).
Applying Periodic Boundaries has no affect on (B) terms but does affect
(U) terms. (U) terms also make use of what is called a non-bond list
that is updated regularly. (UB) terms recognize the Periodic Boundary
but do not require a non-bond list update.
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[4]
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Primarily
an energetic (E) term or primarily a constraint term (C)
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All
modules manage the parameters (force constants) for the term, allowing
for the loading of parameter tables, reading of parameter sets and
assigning new values to parameters. Each module also allows the
creation, modification and deletion of groups of participating atoms.
Finally, the most important function of these modules is to calculate
the contribution of each term to the total potential energy and to the
first derivatives.
Force
Field Assembly
A
molecular model is defined by a potential energy function. To create a
model select the terms that you need and create a module for each. The
modules can be created in any order and more than one instance of a
particular module may be created. Each of the additional instances is
independent of the other. The newly created instances should be saved
in a list. You can manage this list yourself but it is easier to let
the Potential module take care of this.
The newly created modules are empty: Inclusion terms have no
interactions but Exclusion terms assume all pair interactions. Force
Field Assembly is the process of adding interacting groups to Inclusion
terms and adding prohibited groups to the exclusion list of Exclusion
terms. The details vary according to the model class (e.g., all-atom
Protein model, reduced-representation RNA model) and the composition of
the molecule (e.g., the amino-acid sequence, the secondary structure).
This
process can be coded for each class of model. Then to assemble a force
field, one need only supply a high level description of the model
(e.g., amino-acid sequence, secondary structure) to the appropriate
function.
All
Energy modules are located in Yup.Energy.
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