Geometric structure of macromolecules

The geometric structure of the molecule is defined by the locations of each of the atoms and by the specification of the chemical bonds. The atomic locations can be represented as a set of position vectors, f,. It is convenient to encode the chemical bond information as a set of bond vectors,, where each bond vector is calculated as the vector difference between the two position vectors for the bonded atoms Ij = - Fy. 

The values of the bond angles also change with time in a real molecule, but the variations are centered around a well-defined average value. In the following discussion, the bond angles will thus be treated as fixed. 

In a sample containing many macromolecules, each one can have a different set of dihedral angles for the backbone bonds. The internal energy of the chain molecule, E( )y)), depends on the conformation described by the backbone rotation angles. The probability of any particular set depends on 

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