| 1 |
|
| 2 |
\section{The Emperical Energy Functions} |
| 3 |
|
| 4 |
\subsection{Atoms and Molecules} |
| 5 |
|
| 6 |
The basic unit of an {\sc oopse} simulation is the atom. The parameters |
| 7 |
describing the atom are generalized to make the atom as flexible a |
| 8 |
representation as possible. They may represent specific atoms of an |
| 9 |
element, or be used for collections of atoms such as a methyl |
| 10 |
group. The atoms are also capable of having a directional component |
| 11 |
associated with them, often in the form of a dipole. Charges on atoms |
| 12 |
are not currently suporrted by {\sc oopse}. |
| 13 |
|
| 14 |
The second most basic building block of a simulation is the |
| 15 |
molecule. The molecule is a way for {\sc oopse} to keep track of the atoms |
| 16 |
in a simulation in logical manner. This particular unit will store the |
| 17 |
identities of all the atoms associated with itself and is responsible |
| 18 |
for the evaluation of its own bonded interaction (i.e.~bonds, bends, |
| 19 |
and torsions). |
