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ConsistentForceField

Guides

  • ConsistentForceField

Tech Notes

  • Extending Coverage of the CFF

Symbols

  • CFFAngle
  • CFFAtomCoordinates
  • CFFDihedral
  • CFFDistance
  • CFFEnergyComponents
  • CFFEnergy
  • CFFEnergyReport
  • CFFGradient
  • CFFHessian
  • CFFNormalModes
  • CFFOptimizeGeometry
  • CFFParameterize
  • CFFThermodynamicFunctions
  • CFFTorsion
  • CFFTwist
  • NormalModeTable
  • $AllowSymbolicCFFEnergy
  • $CFFAuxiliaryParameters
  • $CFFAuxiliaryPatterns
  • $ConsistentForceFieldParameters
  • $ConsistentForceFieldPatterns
RobertNachbar`ConsistentForceField`
CFFParameterize
​
CFFParameterize
[mol,parameters]
returns a new
Molecule
with the key "CFFEnergyLists" added to the
MetaInformation
. The energy lists contain the atom indices and parameter values for the diagonal terms, cross-terms, and constraints used to compute the energy and it derivatives.
​
Details and Options

Examples  
(7)
Basic Examples  
(1)
Parameterize the molecule ethylene:
In[1]:=
mol=
CFFParameterize
[Molecule["C=C"]]
Out[1]=
Molecule
Formula:
C
2
H
4
Atoms:
6
Bonds:
5

Examine the energy lists stored in the MetaInformation:
In[2]:=
mol["MetaInformation"]["CFFEnergyLists"]
Out[2]=
Atoms{C,C,H,H,H,H},Stretch{{{1,2},1309.9,1.333},{{1,3},723.,1.089},{{1,4},723.,1.089},{{2,5},723.,1.089},{{2,6},723.,1.089}},Bend{{{2,1,3},67.5,2.11534},{{2,1,4},67.5,2.11534},{{3,1,4},66.7,2.05251},{{1,2,5},67.5,2.11534},{{1,2,6},67.5,2.11534},{{5,2,6},66.7,2.05251}},Torsion{},Twist{{{{3,4},1,2,{6,5}},37.9}},OutOfPlane{{{1,2,3,4},22.9},{{2,1,6,5},22.9}},Nonbond{{{3,5},0.00410881,3.632},{{3,6},0.00410881,3.632},{{4,5},0.00410881,3.632},{{4,6},0.00410881,3.632}},StretchStretch{},StretchBend{{{1,2,5},38.4,1.333,2.11534},{{1,2,6},38.4,1.333,2.11534},{{2,1,3},38.4,1.333,2.11534},{{2,1,4},38.4,1.333,2.11534}},BendBend{{{1,2,5,6},-7.9,2.11534,2.11534},{{2,1,3,4},-7.9,2.11534,2.11534}},BendBendTwist{{{3,1,2,6},-10.,2.11534,2.11534},{{3,1,2,5},-10.,2.11534,2.11534},{{4,1,2,6},-10.,2.11534,2.11534},{{4,1,2,5},-10.,2.11534,2.11534}},OopOop{{{{3,4},1,2,{6,5}},3.31}},Constraint{}
Options  
(5)

Applications  
(1)

SeeAlso
$CFFAuxiliaryPatterns
 
▪
$CFFAuxiliaryParameters
TechNotes
▪
Extending the CFF Coverage
RelatedGuides
▪
ConsistentForceField
RelatedLinks
https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
""

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