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\section{\label{sec:DUFF}Dipolar Unified-Atom Force Field} |
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The \underline{D}ipolar \underline{U}nified-Atom |
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\underline{F}orce \underline{F}ield (DUFF) was developed to |
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\underline{F}orce \underline{F}ield ({\sc duff}) was developed to |
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simulate lipid bilayers. We needed a model capable of forming |
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bilayers, while still being sufficiently computationally efficient to |
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allow simulations of large systems ($\approx$100's of phospholipids, |
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computationally expensive Ewald-Sum. Instead, we can use |
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neighbor-lists and cutoff radii for the dipolar interactions. |
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As an example, lipid head groups in DUFF are represented as point |
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As an example, lipid head groups in {\sc duff} are represented as point |
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dipole interaction sites.PC and PE Lipid head groups are typically |
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zwitterionic in nature, with charges separated by as much as |
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6~$\mbox{\AA}$. By placing a dipole of 20.6~Debye at the head group |
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atom in Fig.~\ref{fig:lipidModel}. |
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\begin{figure} |
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\includegraphics[angle=-90,width=\linewidth]{lipidModel.epsi} |
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\epsfxsize=6in |
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\epsfbox{lipidModel.epsi} |
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\caption{A representation of the lipid model. $\phi$ is the torsion angle, $\theta$ % |
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is the bend angle, $\mu$ is the dipole moment of the head group, and n is the chain length.} |
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\label{fig:lipidModel} |
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used when integrating the equations of motion. |
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\subsection{\label{subSec:energyFunctions}DUFF Energy Functions} |
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\subsection{\label{subSec:energyFunctions}{\sc duff} Energy Functions} |
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The total energy of function in DUFF is given by the following: |
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The total energy of function in {\sc duff} is given by the following: |
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\begin{equation} |
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V_{\text{Total}} = \sum^{N}_{I=1} V^{I}_{\text{Internal}} |
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+ \sum^{N}_{I=1} \sum^{N}_{J=1} V^{IJ}_{\text{Cross}} |
