The energy and properties of a single molecular geometry of a
system are of limited interest, especially as the size of the system
increases. In consequence, a wide range of techniques has been developed
to explore the conformations that are accessible to a system. Some
of the most basic of these are local geometry optimization
algorithms that aim to locate structures of low potential energy.
pDynamo has a number of geometry optimization methods, one of which — a
conjugate gradient algorithm — is illustrated in the program
# . Define the molecule and its QC model.
molecule = XYZFile_ToSystem ( os.path.join ( xyzPath, "bala_c7eq.xyz" ) )
molecule.DefineQCModel ( QCModelMNDO ( "am1" ) )
molecule.Summary ( )
# . Save a copy of the starting coordinates.
coordinates3 = Clone ( molecule.coordinates3 )
# . Determine the starting energy.
eStart = molecule.Energy ( )
# . Optimization.
ConjugateGradientMinimize_SystemGeometry ( molecule ,
logFrequency = 100 ,
maximumIterations = 2000 ,
rmsGradientTolerance = 0.1 )
# . Determine the final energy.
eStop = molecule.Energy ( )
# . Determine the RMS coordinate deviation between the optimized and unoptimized structures.
masses = molecule.atoms.GetItemAttributes ( "mass" )
coordinates3.Superimpose ( molecule.coordinates3, weights = masses )
rms = coordinates3.RMSDeviation ( molecule.coordinates3, weights = masses )
# . Print the results.
table = logFile.GetTable ( columns = [ 30, 30 ] )
table.Start ( )
table.Title ( "Minimization Results" )
table.Entry ( "Energy Change", alignment = "l" )
table.Entry ( "%20.4f" % ( eStop - eStart, ) )
table.Entry ( "RMS Coordinate Deviation", alignment = "l" )
table.Entry ( "%20.4f" % ( rms, ) )
table.Stop ( )
The program employs a semi-empirical QC method to geometry
optimize a conformation of the bALA molecule. After the optimization,
the difference in energy between the starting, unoptimized and final,
optimized structures is printed along with their RMS coordinate
- The bALA molecule has a number of different stable
conformations. One way of exploring these is to generate a
two-dimensional map of the molecule's conformational space as a function
of its φ and ψ dihedral angles. Using pDynamo's dihedral soft
capability, generate such a φ/ψ map by performing
geometry optimizations with different constrained values of the φ and ψ
angles. Identify the stable regions on the surface and the low energy
paths that go between them. Examples of how to use soft constraints may be found in the programs