Practical Considerations

It should be clear that force field methods are models of the real quantum mechanical systems. The neglect of electrons as individual particles forces the user to define explicitly the bonding in the molecule prior to any calculations. The user must decide how to describe a given molecule in terms of the selected force field. The input to a calculation consists of three sets of information:

(1) Which atom types are present?

(2) How are they connected, i.e. which atoms are bonded to each other?

(3) A start guess of the geometry.

The first two sets of information determine the functional form of EFF, i.e. enable the calculation of the potential energy surface for the molecule. Normally the molecule will then be optimized by minimizing EFF, which requires a starting guess of the geometry. The information necessary for the program to perform the calculation is read via a file on the computer, and in older programs, the input file had to be prepared manually by the user. All the above three sets of information, however, can be uniquely defined from a (three-dimensional) drawing of a molecule. Modern programs therefore have a graphical interface that allows the molecule simply to be drawn on the screen or constructed from pre-optimized fragments. The interface then automatically assigns suitable atom types based on the selected atomic symbols and the connectivity, and converts the drawing to Cartesian coordinates.

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