| 57 |
|
In a typical bilayer simulation, the dominant portion of the |
| 58 |
|
computation time will be spent calculating water-water interactions. |
| 59 |
|
As an efficient solvent model, the Soft Sticky Dipole (SSD) water |
| 60 |
< |
model\cite{Chandra1999,Fennel2004} is used as the explicit solvent |
| 60 |
> |
model\cite{Chandra1999,Fennell2004} is used as the explicit solvent |
| 61 |
|
in this project. Unlike other water models which have partial |
| 62 |
|
charges distributed throughout the whole molecule, the SSD water |
| 63 |
|
model consists of a single site which is a Lennard-Jones interaction |
| 315 |
|
\label{lipidFigure:bilayer} |
| 316 |
|
\end{figure} |
| 317 |
|
|
| 318 |
< |
\subsubsection{Electron Density Profile (EDP)} |
| 318 |
> |
\subsubsection{\textbf{Electron Density Profile (EDP)}} |
| 319 |
|
|
| 320 |
|
Assuming a gaussian distribution of electrons on each atomic center |
| 321 |
|
with a variance estimated from the size of the van der Waals radius, |
| 351 |
|
\label{lipidFigure:electronDensity} |
| 352 |
|
\end{figure} |
| 353 |
|
|
| 354 |
< |
\subsubsection{$\text{S}_{\text{{\sc cd}}}$ Order Parameter} |
| 354 |
> |
\subsubsection{\textbf{$\text{S}_{\text{{\sc cd}}}$ Order Parameter}} |
| 355 |
|
|
| 356 |
|
Measuring deuterium order parameters by NMR is a useful technique to |
| 357 |
|
study the orientation of hydrocarbon chains in phospholipids. The |
