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\section{The Emperical Energy Functions} |
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\subsection{Atoms and Molecules} |
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The basic unit of an OOPSE simulation is the atom. The parameters |
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describing the atom are generalized to make the atom as flexible a |
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representation as possible. They may represent specific atoms of an |
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element, or be used for collections of atoms such as a methyl |
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group. The atoms are also capable of having a directional component |
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associated with them, often in the form of a dipole. Charges on atoms |
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are not currently suporrted by OOPSE. |
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The second most basic building block of a simulation is the |
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molecule. The molecule is a way for OOPSE to keep track of the atoms |
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in a simulation in logical manner. This particular unit will store the |
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identities of all the atoms associated with itself and is responsible |
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for the evaluation of its own bonded interaction (i.e.~bonds, bends, |
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and torsions). |
