--- trunk/mattDisertation/oopse.tex	2004/04/14 20:30:03	1111
+++ trunk/mattDisertation/oopse.tex	2004/04/15 02:45:10	1112
@@ -233,7 +233,7 @@ $\epsilon_{ij}$ scales the well depth of the potential
 Where $r_{ij}$ is the distance between particles $i$ and $j$,
 $\sigma_{ij}$ scales the length of the interaction, and
 $\epsilon_{ij}$ scales the well depth of the potential. Scheme
-\ref{sch:LJFF} gives and example \texttt{.bass} file that
+\ref{sch:LJFF} gives an example \texttt{.bass} file that
 sets up a system of 108 Ar particles to be simulated using the
 Lennard-Jones force field.
 
@@ -264,7 +264,7 @@ the equations of motion.
 the energy value at $r_{\text{cut}}$ is subtracted from the
 potential. This causes the potential to go to zero smoothly at the
 cut-off radius, and preserves conservation of energy in integrating
-the equations of motion.
+the equations of motion. There still remains a discontinuity in the derivative (the forces), however, this does not significantly affect the dynamics.
 
 Interactions between dissimilar particles requires the generation of
 cross term parameters for $\sigma$ and $\epsilon$. These are
@@ -381,9 +381,7 @@ potential are excluded for pairs that are closer than 
 Here $V_{\text{bend}}$ is the bend potential for all 1, 3 bonded pairs
 within the molecule $I$, and $V_{\text{torsion}}$ is the torsion potential
 for all 1, 4 bonded pairs. The pairwise portions of the internal
-potential are excluded for pairs that are closer than three bonds,
-i.e.~atom pairs farther away than a torsion are included in the
-pair-wise loop.
+potential are excluded for atom pairs that are involved in the same bond, bend, or torsion. All other atom pairs within the molecule are subject to the LJ pair potential.
 
 
 The bend potential of a molecule is represented by the following function:
@@ -573,7 +571,7 @@ model. Solvent parameters can be easily modified in an
 exhibits improved liquid structure and transport behavior. If the use
 of a reaction field long-range interaction correction is desired, it
 is recommended that the parameters be modified to those of the SSD/RF
-model. Solvent parameters can be easily modified in an accompanying
+model (an SSD variant  parameterized for reaction field). Solvent parameters can be easily modified in an accompanying
 \texttt{.bass} file as illustrated in the scheme below. A table of the
 parameter values and the drawbacks and benefits of the different
 density corrected SSD models can be found in
@@ -1658,7 +1656,7 @@ solving the Lagrange multipliers of constraint. The sy
 oopse}, we have implemented the {\sc rattle} algorithm of
 Andersen.\cite{andersen83} The algorithm is a velocity verlet
 formulation of the {\sc shake} method\cite{ryckaert77} of iteratively
-solving the Lagrange multipliers of constraint. The system of lagrange
+solving the Lagrange multipliers of constraint. The system of Lagrange
 multipliers allows one to reformulate the equations of motion with
 explicit constraint forces.\cite{fowles99:lagrange} 
 
@@ -2231,7 +2229,7 @@ calculated between the two blocks. this second block i
 \texttt{dynamicProps} will calculate all of the time correlation frame
 pairs within the block. After in-block correlations are complete, a
 second block of the trajectory is read, and the cross correlations are
-calculated between the two blocks. this second block is then freed and
+calculated between the two blocks. This second block is then freed and
 then incremented and the process repeated until the end of the
 trajectory. Once the end is reached, the first block is freed then
 incremented, and the again the internal time correlations are
@@ -2261,7 +2259,7 @@ program. Allowing researchers to not only benefit from
 z-constraint method.
 
 These features are all brought together in a single open-source
-program. Allowing researchers to not only benefit from
+program. This allows researchers to not only benefit from
 {\sc oopse}, but also contribute to {\sc oopse}'s development as
 well.