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\section{Initial Simulations} |
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\label{sec:initialSimulations} |
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The first simulations we performed, were two lipid/water systems. The |
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first was a simulation of 25 lipids and 1386 waters in a cubic |
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box. The second simulation was 50 lipids and 1384 waters in a |
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rectangular box. Both systems were integrated in the microcanonical |
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ensemble for times in excess of 15 ns. |
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|
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The 25 lipid system (scheme I) was initially started from an ordered |
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configuration. The lipids were aligned in a 5x5 square with a side by |
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side spacing of $\approx\mbox{8\AA}$ (Fig.~\ref{fig:25lipidInit}) The |
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box was then filled with water in an FCC lattice. The temperature was |
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then equilibrated to 300~K by resampling the atomic velocitiues from a |
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Maxwell-Boltzmann distribution. Once the temperature had been set, the |
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system was allowed to progress for $\approx 20$~ns. |
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|
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\begin{figure} |
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\parbox{\linewidth}{Here is the initial 25 lipid configuration} |
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\caption[The initial configuration of scheme I]{The starting configuration of scheme I.} |
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\label{fig:25lipidinit} |
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\end{figure} |
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The 50 lipid system (scheme II) was initially started from a randomly |
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generarted configuration. A system box was initially filled with water |
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in an FCC lattice. The 50 lipid molecules were then sequentially |
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placed in the box with a random orientaion and position. If the lipid |
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did not overlap with a previously placed one, its position was |
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accepted, and the next lipid was placed. Once all 50 lipids were |
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positioned, any waters overlaping with the lipids were removed |
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(Fig.~\ref{fig:r50Init}. The system was then equilibrated to 300~K in |
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the same manner as scheme I. |
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|
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\begin{figure} |
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\parbox{\linewidth}{Here is the initial random 50 lipid configuration} |
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\caption[The initial configuration of scheme II]{The starting configuration of scheme II.} |
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\label{fig:r50Init} |
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\end{figure} |
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|
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\subsection{Results} |
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\label{subSec:initSimsResults} |
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|
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Scheme I was found to split into two leaves within the first |
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5~ns. However, as the simulation progressed, it became appaarent that |
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the system was frustrated in its confined box. After 15~ns, the two |
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leaveswere still unable to form a bilayer. Instead, thew were only |
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able to form two skewed layers (Fig.~\ref{fig:25lipidFinal}). |
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|
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\begin{figure} |
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\parbox{\linewidth}{Here is the final 25 lipid configuration} |
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\caption[The final configuration of scheme I]{The final configuration of scheme I.} |
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\label{fig:25lipidFinal} |
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\end{figure} |
