--- trunk/chrisDissertation/Introduction.tex 2006/09/21 23:21:37 3016 +++ trunk/chrisDissertation/Introduction.tex 2006/09/22 13:45:24 3019 @@ -53,7 +53,7 @@ motion, and one useful formulation of them is the Lagr time $t_2$. To find out, we need the classical equations of motion, and one useful formulation of them is the Lagrangian form. -The Lagrangian ($L$) is a function of the positions and velocites that +The Lagrangian ($L$) is a function of the positions and velocities that takes the form, \begin{equation} L = K - V, @@ -542,7 +542,7 @@ switching transition. that the higher the order of the polynomial, the more abrupt the switching transition. -\subsection{Long-Range Interaction Corrections} +\subsection{\label{sec:LJCorrections}Long-Range Interaction Corrections} While a good approximation, accumulating interaction only from the nearby particles can lead to some issues, because the further away @@ -574,7 +574,7 @@ In typical molecular dynamics simulations there are no \subsection{Periodic Boundary Conditions} In typical molecular dynamics simulations there are no restrictions -placed on the motion of particles outside of what the interparticle +placed on the motion of particles outside of what the inter-particle interactions dictate. This means that if a particle collides with other particles, it is free to move away from the site of the collision. If we consider the entire system as a collection of @@ -666,7 +666,7 @@ simulations. In section \ref{sec:t5peThermo}, we use f property can be determined via the standard deviation. Fluctuations are useful for measuring various thermodynamic properties in computer simulations. In section \ref{sec:t5peThermo}, we use fluctuations in -propeties like the enthalpy and volume to calculate various +properties like the enthalpy and volume to calculate various thermodynamic properties, such as the constant pressure heat capacity and the isothermal compressibility.