--- trunk/ssdePaper/nptSSD.tex	2003/09/03 21:36:09	743
+++ trunk/ssdePaper/nptSSD.tex	2003/09/10 22:42:57	759
@@ -23,7 +23,7 @@
 
 \begin{document}
 
-\title{On the temperature dependent structural and transport properties of the soft sticky dipole (SSD) and related single point water models}
+\title{On the temperature dependent properties of the soft sticky dipole (SSD) and related single point water models}
 
 \author{Christopher J. Fennell and J. Daniel Gezelter{\thefootnote}
 \footnote[1]{Corresponding author. \ Electronic mail: gezelter@nd.edu}}
@@ -154,19 +154,27 @@ Up to this point, a detailed look at the model's struc
 scale biological systems, such as membrane phase behavior, a specific
 interest within our group.
 
-Up to this point, a detailed look at the model's structure and ion
-solvation abilities has been performed.\cite{Ichiye96} In addition, a
-thorough investigation of the dynamic properties of SSD was performed
-by Chandra and Ichiye focusing on translational and orientational
-properties at 298 K.\cite{Ichiye99} This study focuses on determining
-the density maximum for SSD utilizing both microcanonical and
-isobaric-isothermal ensemble molecular dynamics, while using the
-reaction field method for handling long-ranged dipolar interactions. A
-reaction field method has been previously implemented in Monte Carlo
-simulations by Liu and Ichiye in order to study the static dielectric
-constant for the model.\cite{Ichiye96b} This paper will expand the
-scope of these original simulations to look on how the reaction field
-affects the physical and dynamic properties of SSD systems.
+One of the key limitations of this water model, however, is that it
+has been parameterized for use with the Ewald Sum technique for the
+handling of long-ranged interactions.  When studying very large
+systems, the Ewald summation and even particle-mesh Ewald become
+computational burdens with their respective ideal $N^\frac{3}{2}$ and
+$N\log N$ calculation scaling orders for $N$ particles.\cite{Darden99}
+In applying this water model in these types of systems, it would be
+useful to know its properties and behavior with the more
+computationally efficient reaction field (RF) technique, and even with
+a cutoff that lacks any form of long range correction. This study
+addresses these issues by looking at the structural and transport
+behavior of SSD over a variety of temperatures, with the purpose of
+utilizing the RF correction technique. Towards the end, we suggest
+alterations to the parameters that result in more water-like
+behavior. It should be noted that in a recent publication, some the
+original investigators of the SSD water model have put forth
+adjustments to the original SSD water model to address abnormal
+density behavior (also observed here), calling the corrected model
+SSD1.\cite{Ichiye03} This study will consider this new model's
+behavior as well, and hopefully improve upon its depiction of water
+under conditions without the Ewald Sum.
 
 \section{Methods}
 
@@ -225,11 +233,11 @@ in energy conservation. There is still the issue of an
 nine elements long as opposed to 3 or 4 elements for Euler angles and
 quaternions respectively. System memory has become much less of an
 issue in recent times, and this has resulted in substantial benefits
-in energy conservation. There is still the issue of an additional 5 or
-6 additional elements for describing the orientation of each particle,
-which will increase dump files substantially. Simply translating the
-rotation matrix into its component Euler angles or quaternions for
-storage purposes relieves this burden.
+in energy conservation. There is still the issue of 5 or 6 additional
+elements for describing the orientation of each particle, which will
+increase dump files substantially. Simply translating the rotation
+matrix into its component Euler angles or quaternions for storage
+purposes relieves this burden.
 
 The symplectic splitting method allows for Verlet style integration of
 both linear and angular motion of rigid bodies. In the integration
@@ -237,10 +245,10 @@ particle simulation shows a 7\% increase in simulation
 evaluations to update the rotation matrix.\cite{Dullweber1997} These
 matrix rotations end up being more costly computationally than the
 simpler arithmetic quaternion propagation. On average, a 1000 SSD
-particle simulation shows a 7\% increase in simulation time using the
+particle simulation shows a 7\% increase in computation time using the
 symplectic step method in place of quaternions. This cost is more than
 justified when comparing the energy conservation of the two methods as
-illustrated in figure \ref{timestep}.
+illustrated in figure \ref{timestep}. 
 
 \begin{figure}
 \includegraphics[width=61mm, angle=-90]{timeStep.epsi}
@@ -262,7 +270,9 @@ demonstrated.
 with the quaternion method showing a slight energy drift over time in
 the 0.5 fs time step simulation. At time steps of 1 and 2 fs, the
 energy conservation benefits of the symplectic step method are clearly
-demonstrated.
+demonstrated. Thus, while maintaining the same degree of energy
+conservation, one can take considerably longer time steps, leading to
+an overall reduction in computation time.
 
 Energy drift in these SSD particle simulations was unnoticeable for
 time steps up to three femtoseconds. A slight energy drift on the
