--- trunk/oopsePaper/DUFF.tex	2003/08/24 04:00:44	716
+++ trunk/oopsePaper/DUFF.tex	2003/08/25 20:25:12	717
@@ -4,7 +4,7 @@ model capable of forming bilaers, while still being su
 The DUFF (\underline{D}ipolar \underline{U}nified-atom
 \underline{F}orce \underline{F}ield) force field was developed to
 simulate lipid bilayer formation and equilibrium dynamics. We needed a
-model capable of forming bilaers, while still being sufficiently
+model capable of forming bilayers, while still being sufficiently
 computationally efficient allowing simulations of large systems
 (\~100's of phospholipids, \~1000's of waters) for long times (\~10's
 of nanoseconds).
@@ -35,11 +35,11 @@ seperated by only 5 to 6~$\mbox{\AA}$. By placing a di
 Applying this standard to the lipid model, we decided to represent the
 lipid model as a point dipole interaction site. Lipid head groups are
 typically zwitterionic in nature, with sometimes full integer charges
-seperated by only 5 to 6~$\mbox{\AA}$. By placing a dipole of
+separated by only 5 to 6~$\mbox{\AA}$. By placing a dipole of
 20.6~Debye at the head groups center of mass, our model mimics the
-dipole of DMPC.\cite{Cevc87} Then, to account for the steric henderanc
-of the head group, a Lennard-Jones interaction site is also oacted at
-the psuedoatom's center of mass. The model is illustrated in
+dipole of DMPC.\cite{Cevc87} Then, to account for the steric hindrance
+of the head group, a Lennard-Jones interaction site is also located at
+the pseudoatom's center of mass. The model is illustrated in
 Fig.~\ref{fig:lipidModel}.
 
 \begin{figure}
@@ -56,22 +56,47 @@ an alkyl chain to keep the number of pseudoatoms to a 
 unified-atom representation of n-alkanes. It is parametrized against
 phase equilibria using Gibbs Monte Carlo simulation techniques. One of
 the advantages of TraPPE is that is generalizes the types of atoms in
-an alkyl chain to keep the number of pseudoatoms to a minimum.
-%( $ \mbox{CH_3} $ %-$\mathbf{\mbox{CH_2}}$-$\mbox{CH_3}$ is the same as
+an alkyl chain to keep the number of pseudoatoms to a minimum; the
+$\mbox{CH}_2$ in propane is the same as the central and offset
+$\mbox{CH}_2$'s in pentane, meaning the pseudoatom type does not
+change according to the atom's environment.
 
 Another advantage of using TraPPE is the constraining of all bonds to
 be of fixed length. Typically, bond vibrations are the motions in a
-molecular dynamic simulation. This neccesitates a small time step
+molecular dynamic simulation. This necessitates a small time step
 between force evaluations be used to ensure adequate sampling of the
 bond potential. Failure to do so will result in loss of energy
 conservation within the microcanonical ensemble. By constraining this
 degree of freedom, time steps larger than were previously allowable
 are able to be used when integrating the equations of motion.
 
+After developing the model for the phospholipids, we needed a model
+for water that would complement our lipid. For this we turned to the
+soft sticky dipole (SSD) model of Ichiye \emph{et
+al.}\cite{liu96:new_model} This model is discussed in greater detail
+in Sec.~\ref{sec:SSD}. The basic idea of the model is to reduce water
+to a single Lennard-Jones interaction site. The site also contains a
+dipole to mimic the partial charges on the hydrogens and the
+oxygen. However, what makes the SSD model unique is the inclusion of a
+tetrahedral short range potential to recover the hydrogen bonding of
+water, an important factor when modeling bilayers, as it has been
+shown that hydrogen bond network formation is a leading contribution
+to the entropic driving force towards lipid bilayer
+formation.\cite{Cevc87}
+
+BREAK 
+
+END OF CURRENT REVISIONS 
+
+BREAK
+
+
+
+
+
 The main energy function in OOPSE is DUFF (the Dipolar Unified-atom
 Force Field). DUFF is a collection of parameters taken from Seipmann
- and Ichiye \emph{et
-al.}\cite{liu96:new_model} The total energy of interaction is given by
+ and  The total energy of interaction is given by
 Eq.~\ref{eq:totalPotential}:
 \begin{equation}
 V_{\text{Total}} =
@@ -102,7 +127,7 @@ $\phi$. This prevents the need for repeated trigonemtr
 \end{equation}
 Here, the authors decided to use a potential in terms of a power
 expansion in $\cos \phi$ rather than the typical expansion in
-$\phi$. This prevents the need for repeated trigonemtric
+$\phi$. This prevents the need for repeated trigonometric
 evaluations. Again, all $k_n$ constants were based on those in TraPPE.
 
 \subsection{Non-Bonded Interactions}
