| 229 |
|
Where $k_{\theta}$ sets the stiffness of the bend potential, and $\theta_0$ |
| 230 |
|
sets the equilibrium bend angle. The torsion potential was given by: |
| 231 |
|
\begin{equation} |
| 232 |
< |
V_{\text{tors.}}(\phi_{ijkl})= \cos(\phi_{ijkl}) |
| 232 |
> |
V_{\text{tors.}}(\phi_{ijkl})= c_1[1+\cos\phi] |
| 233 |
> |
+ c_2 [1 - \cos(2\phi)] + c_3[1 + \cos(3\phi)] |
| 234 |
|
\label{eq:torsPot} |
| 235 |
|
\end{equation} |
| 236 |
< |
Here, ``blank'' controls the scaling of the torsion potential, and the |
| 237 |
< |
$c$ terms are paramterized for the $\cos$ expansion. All parameters |
| 238 |
< |
for bonded and non-bonded potentials in the tail atoms were taken from |
| 239 |
< |
TraPPE.\cite{Siepmann1998} The bonded interactions for the head atom |
| 240 |
< |
were also taken from TraPPE, however it's dipole moment and mass were |
| 241 |
< |
based on the properties of ``DMPC?'''s head group. The Lennard-Jones |
| 242 |
< |
parameter for the Head group was chosen such that it was roughly twice |
| 242 |
< |
the size of a $\text{CH}_3$ atom, and it's well depth was set to be |
| 243 |
< |
aproximately equal to that of $\text{CH}_3$. |
| 236 |
> |
All parameters for bonded and non-bonded potentials in the tail atoms |
| 237 |
> |
were taken from TraPPE.\cite{Siepmann1998} The bonded interactions for |
| 238 |
> |
the head atom were also taken from TraPPE, however it's dipole moment |
| 239 |
> |
and mass were based on the properties of ``DMPC?'''s head group. The |
| 240 |
> |
Lennard-Jones parameter for the head group was chosen such that it was |
| 241 |
> |
roughly twice the size of a $\text{CH}_3$ atom, and it's well depth |
| 242 |
> |
was set to be aproximately equal to that of $\text{CH}_3$. |
| 243 |
|
|
| 244 |
< |
\section{Simulations} |
| 245 |
< |
\subsection{25 lipids in water} |
| 244 |
> |
\section{Initial Simulation: 25 lipids in water} |
| 245 |
> |
\label{sec:5x5} |
| 246 |
|
|
| 247 |
< |
\subsection{50 randomly oriented lipids in water} |
| 247 |
> |
\subsection{Starting Configurtion and Parameters} |
| 248 |
> |
\label{sec:5x5Start} |
| 249 |
> |
|
| 250 |
> |
\begin{floatingfigure}{85mm} |
| 251 |
> |
\includegraphics[width=75mm]{5x5-initial.eps} |
| 252 |
> |
\caption{A snapshot of the initial configuration of the 25 lipid simulation.} |
| 253 |
> |
\label{fig:5x5Start} |
| 254 |
> |
\end{floatingfigure} |
| 255 |
> |
|
| 256 |
> |
Our first simulation was an array of 25 single chained lipids in a sea |
| 257 |
> |
of water (Figure \ref{fig:5x5Start}). The total number of water |
| 258 |
> |
molecules was 1386, giving a final of water concentration of 70\% |
| 259 |
> |
wt. The simulation box measured 34.5~$\mbox{\AA}$ x 39.4~$\mbox{\AA}$ |
| 260 |
> |
x 39.4~$\mbox{\AA}$ with periodic boundry connditions invoked. The |
| 261 |
> |
system was simulated in the micro-canonical (NVE) ensemble with an |
| 262 |
> |
average temperature of 300~K. |
| 263 |
> |
|
| 264 |
> |
|
| 265 |
> |
yada |
| 266 |
> |
|
| 267 |
> |
yada |
| 268 |
|
|
| 269 |
+ |
yada |
| 270 |
+ |
yya |
| 271 |
+ |
d |
| 272 |
+ |
|
| 273 |
+ |
uada |
| 274 |
+ |
|
| 275 |
+ |
adsd |
| 276 |
+ |
|
| 277 |
+ |
asfa |
| 278 |
+ |
|
| 279 |
+ |
asfdads |
| 280 |
+ |
|
| 281 |
+ |
\subsection{Results} |
| 282 |
+ |
\label{sec:5x5Results} |
| 283 |
+ |
|
| 284 |
+ |
|
| 285 |
+ |
Figure \ref{fig:5x5Final} shows a snapshot of the system at |
| 286 |
+ |
3.6~ns. Here the bylayer has formed with the lipid chains tilted to |
| 287 |
+ |
the bylayer normal. |
| 288 |
+ |
|
| 289 |
+ |
yada |
| 290 |
+ |
|
| 291 |
+ |
yada |
| 292 |
+ |
|
| 293 |
+ |
yada |
| 294 |
+ |
|
| 295 |
+ |
yada |
| 296 |
+ |
|
| 297 |
+ |
%\begin{floatingfigure}{85mm} |
| 298 |
+ |
%\includegraphics[angle=-90,width=75mm]{5x5-3.6ns.epsi} |
| 299 |
+ |
%\caption{A snapshot of the system at 3.6~ns.\vspace{5mm}} |
| 300 |
+ |
%\label{fig:5x5Final} |
| 301 |
+ |
%\end{floatingfigure} |
| 302 |
+ |
|
| 303 |
+ |
|
| 304 |
+ |
|
| 305 |
+ |
|
| 306 |
+ |
\section{Second Simulation: 50 randomly oriented lipids in water} |
| 307 |
+ |
|
| 308 |
+ |
the second simulation |
| 309 |
+ |
|
| 310 |
|
\section{Preliminary Results} |
| 311 |
|
|
| 312 |
|
\section{Discussion} |
