mattDisertation/collections/initalSimulations.tex


\section{Initial Simulations}
\label{sec:initialSimulations}

The first simulations we performed, were two lipid/water systems. The
first was a simulation of 25 lipids and 1386 waters in a cubic
box. The second simulation was 50 lipids and 1384 waters in a
rectangular box. Both systems were integrated in the microcanonical
ensemble for times in excess of 15 ns.

The 25 lipid system (scheme I) was initially started from an ordered
configuration. The lipids were aligned in a 5x5 square with a side by
side spacing of $\approx\mbox{8\AA}$ (Fig.~\ref{fig:25lipidInit}) The
box was then filled with water in an FCC lattice. The temperature was
then equilibrated to 300~K by resampling the atomic velocitiues from a
Maxwell-Boltzmann distribution. Once the temperature had been set, the
system was allowed to progress for $\approx 20$~ns.

\begin{figure}
\parbox{\linewidth}{Here is the initial 25 lipid configuration}
\caption[The initial configuration of scheme I]{The starting configuration of scheme I.}
\label{fig:25lipidinit}
\end{figure}

The 50 lipid system (scheme II) was initially started from a randomly
generarted configuration. A system box was initially filled with water
in an FCC lattice. The 50 lipid molecules were then sequentially
placed in the box with a random orientaion and position. If the lipid
did not overlap with a previously placed one, its position was
accepted, and the next lipid was placed. Once all 50 lipids were
positioned, any waters overlaping with the lipids were removed
(Fig.~\ref{fig:r50Init}. The system was then equilibrated to 300~K in
the same manner as scheme I.

\begin{figure}
\parbox{\linewidth}{Here is the initial random 50 lipid configuration}
\caption[The initial configuration of scheme II]{The starting configuration of scheme II.}
\label{fig:r50Init}
\end{figure}

\subsection{Results}
\label{subSec:initSimsResults}

Scheme I was found to split into two leaves within the first
5~ns. However, as the simulation progressed, it became appaarent that
the system was frustrated in its confined box. After 15~ns, the two
leaveswere still unable to form a bilayer. Instead, thew were only
able to form two skewed layers (Fig.~\ref{fig:25lipidFinal}).

\begin{figure} 
\parbox{\linewidth}{Here is the final 25 lipid configuration} 
\caption[The final configuration of scheme I]{The final configuration of scheme I.}
\label{fig:25lipidFinal}
\end{figure}
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2			\section{Initial Simulations}
3			\label{sec:initialSimulations}
4
5			The first simulations we performed, were two lipid/water systems. The
6			first was a simulation of 25 lipids and 1386 waters in a cubic
7			box. The second simulation was 50 lipids and 1384 waters in a
8			rectangular box. Both systems were integrated in the microcanonical
9			ensemble for times in excess of 15 ns.
10
11			The 25 lipid system (scheme I) was initially started from an ordered
12			configuration. The lipids were aligned in a 5x5 square with a side by
13			side spacing of $\approx\mbox{8\AA}$ (Fig.~\ref{fig:25lipidInit}) The
14			box was then filled with water in an FCC lattice. The temperature was
15			then equilibrated to 300~K by resampling the atomic velocitiues from a
16			Maxwell-Boltzmann distribution. Once the temperature had been set, the
17			system was allowed to progress for $\approx 20$~ns.
18
19			\begin{figure}
20			\parbox{\linewidth}{Here is the initial 25 lipid configuration}
21			\caption[The initial configuration of scheme I]{The starting configuration of scheme I.}
22			\label{fig:25lipidinit}
23			\end{figure}
24
25			The 50 lipid system (scheme II) was initially started from a randomly
26			generarted configuration. A system box was initially filled with water
27			in an FCC lattice. The 50 lipid molecules were then sequentially
28			placed in the box with a random orientaion and position. If the lipid
29			did not overlap with a previously placed one, its position was
30			accepted, and the next lipid was placed. Once all 50 lipids were
31			positioned, any waters overlaping with the lipids were removed
32			(Fig.~\ref{fig:r50Init}. The system was then equilibrated to 300~K in
33			the same manner as scheme I.
34
35			\begin{figure}
36			\parbox{\linewidth}{Here is the initial random 50 lipid configuration}
37			\caption[The initial configuration of scheme II]{The starting configuration of scheme II.}
38			\label{fig:r50Init}
39			\end{figure}
40
41			\subsection{Results}
42			\label{subSec:initSimsResults}
43
44			Scheme I was found to split into two leaves within the first
45			5~ns. However, as the simulation progressed, it became appaarent that
46			the system was frustrated in its confined box. After 15~ns, the two
47			leaveswere still unable to form a bilayer. Instead, thew were only
48			able to form two skewed layers (Fig.~\ref{fig:25lipidFinal}).
49
50			\begin{figure}
51			\parbox{\linewidth}{Here is the final 25 lipid configuration}
52			\caption[The final configuration of scheme I]{The final configuration of scheme I.}
53			\label{fig:25lipidFinal}
54			\end{figure}