Copt

This is an implementation of the molecular energy as a function of Cartesian coordinates.

It must be passed a coords= argument and the type of computation to be used to generate the energy, gradients, and hessian, (with similar effects to the opt routine).

Argument	Argument type	Mandatory	Default	To specify
coords=	Fragment tag	yes	none	initial geometry
theory=	Energy/Gradient code	yes	none	what type of calculation to perform for energy and gradient
active_atoms=	Tcl List	no	All atoms active	Which atoms are free to move
list_option=	Output keyword	no	medium	Level of output
punchfile=	File name	no	No punchfile generated	File to save sequence of structures generated
result=	Fragment tag	no	copt.result	Where to write the final structure

The variables of the copt function are all Cartesian coordinates, i.e. there are 3N degrees of freedom, (where N is the number of active atoms) because overall rotations and translations are included. For most optimization algorithms this is not a severe problem, but sometimes the soft modes may interfere with convergence.

The following example uses the newopt function to perform a BFGS minimisation of the water molecule with a molecular mechanics energy expression.

#
z_create zmatrix=z {
zmatrix angstrom
o
h 1 oh
h 1 oh 2 hoh
variables 
oh  0.8
hoh 105.0
end
}

z_list zmatrix=z
z_to_c zmatrix=z coords=c

read_input ff {
bond   o h   2000. 1.
angle h o h  300. 100.
}

newopt function=copt: {theory=mm : mm_defs=ff  coords=c}