1 |
mmeineke |
664 |
|
2 |
mmeineke |
713 |
\section{\label{sec:DUFF}The DUFF Force Field} |
3 |
mmeineke |
664 |
|
4 |
mmeineke |
713 |
The DUFF (\underline{D}ipolar \underline{U}nified-atom |
5 |
|
|
\underline{F}orce \underline{F}ield) force field was developed to |
6 |
|
|
simulate lipid bilayer formation and equilibrium dynamics. We needed a |
7 |
|
|
model capable of forming bilaers, while still being sufficiently |
8 |
|
|
computationally efficient allowing simulations of large systems |
9 |
|
|
(\~100's of phospholipids, \~1000's of waters) for long times (\~10's |
10 |
|
|
of nanoseconds). |
11 |
mmeineke |
710 |
|
12 |
mmeineke |
713 |
With this goal in mind, we decided to eliminate all charged |
13 |
|
|
interactions within the force field. Charge distributions were |
14 |
|
|
replaced with dipolar entities, and charge neutral distributions were |
15 |
|
|
reduced to Lennard-Jones interaction sites. This simplification cuts |
16 |
|
|
the length scale of long range interactions from $\frac{1}{r}$ to |
17 |
mmeineke |
716 |
$\frac{1}{r^3}$ (Eq.~\ref{eq:dipole} vs.~ Eq.~\ref{eq:coloumb}), |
18 |
|
|
allowing us to avoid the computationally expensive Ewald-Sum. Instead, |
19 |
|
|
we can use neighbor-lists and cutoff radii for the dipolar |
20 |
|
|
interactions. |
21 |
mmeineke |
710 |
|
22 |
mmeineke |
713 |
\begin{align} |
23 |
|
|
V^{\text{dipole}}_{ij}(\mathbf{r}_{ij},\boldsymbol{\Omega}_{i}, |
24 |
|
|
\boldsymbol{\Omega}_{j}) &= |
25 |
|
|
\frac{1}{4\pi\epsilon_{0}} \biggl[ |
26 |
|
|
\frac{\boldsymbol{\mu}_{i} \cdot \boldsymbol{\mu}_{j}}{r^{3}_{ij}} |
27 |
|
|
- |
28 |
|
|
\frac{3(\boldsymbol{\mu}_i \cdot \mathbf{r}_{ij}) % |
29 |
|
|
(\boldsymbol{\mu}_j \cdot \mathbf{r}_{ij}) } |
30 |
|
|
{r^{5}_{ij}} \biggr]\label{eq:dipole} \\ |
31 |
|
|
V^{\text{ch}}_{ij}(\mathbf{r}_{ij}) &= \frac{q_{i}q_{j}}% |
32 |
|
|
{4\pi\epsilon_{0} r_{ij}} \label{eq:coloumb} |
33 |
|
|
\end{align} |
34 |
|
|
|
35 |
mmeineke |
716 |
Applying this standard to the lipid model, we decided to represent the |
36 |
|
|
lipid model as a point dipole interaction site. Lipid head groups are |
37 |
|
|
typically zwitterionic in nature, with sometimes full integer charges |
38 |
|
|
seperated by only 5 to 6~$\mbox{\AA}$. By placing a dipole of |
39 |
|
|
20.6~Debye at the head groups center of mass, our model mimics the |
40 |
|
|
dipole of DMPC.\cite{Cevc87} Then, to account for the steric henderanc |
41 |
|
|
of the head group, a Lennard-Jones interaction site is also oacted at |
42 |
|
|
the psuedoatom's center of mass. The model is illustrated in |
43 |
|
|
Fig.~\ref{fig:lipidModel}. |
44 |
mmeineke |
713 |
|
45 |
mmeineke |
716 |
\begin{figure} |
46 |
|
|
\includegraphics[angle=-90,width=\linewidth]{lipidModel.epsi} |
47 |
|
|
\caption{A representation of the lipid model. $\phi$ is the torsion angle, $\theta$ % |
48 |
|
|
is the bend angle, $\mu$ is the dipole moment of the head group, and n is the chain length.} |
49 |
|
|
\label{fig:lipidModel} |
50 |
|
|
\end{figure} |
51 |
|
|
|
52 |
|
|
Turning to the tail chains of the phospholipids, we needed a set of |
53 |
|
|
scalable parameters to model the alkyl groups as Lennard-Jones |
54 |
|
|
interaction sites. For this, we used the TraPPE force field of |
55 |
|
|
Siepmann \emph{et al}.\cite{Siepmann1998} The force field is a |
56 |
|
|
unified-atom representation of n-alkanes. It is parametrized against |
57 |
|
|
phase equilibria using Gibbs Monte Carlo simulation techniques. One of |
58 |
|
|
the advantages of TraPPE is that is generalizes the types of atoms in |
59 |
|
|
an alkyl chain to keep the number of pseudoatoms to a minimum. |
60 |
|
|
%( $ \mbox{CH_3} $ %-$\mathbf{\mbox{CH_2}}$-$\mbox{CH_3}$ is the same as |
61 |
|
|
|
62 |
|
|
Another advantage of using TraPPE is the constraining of all bonds to |
63 |
|
|
be of fixed length. Typically, bond vibrations are the motions in a |
64 |
|
|
molecular dynamic simulation. This neccesitates a small time step |
65 |
|
|
between force evaluations be used to ensure adequate sampling of the |
66 |
|
|
bond potential. Failure to do so will result in loss of energy |
67 |
|
|
conservation within the microcanonical ensemble. By constraining this |
68 |
|
|
degree of freedom, time steps larger than were previously allowable |
69 |
|
|
are able to be used when integrating the equations of motion. |
70 |
|
|
|
71 |
|
|
The main energy function in OOPSE is DUFF (the Dipolar Unified-atom |
72 |
|
|
Force Field). DUFF is a collection of parameters taken from Seipmann |
73 |
|
|
and Ichiye \emph{et |
74 |
mmeineke |
664 |
al.}\cite{liu96:new_model} The total energy of interaction is given by |
75 |
mmeineke |
666 |
Eq.~\ref{eq:totalPotential}: |
76 |
mmeineke |
698 |
\begin{equation} |
77 |
|
|
V_{\text{Total}} = |
78 |
|
|
\overbrace{V_{\theta} + V_{\phi}}^{\text{bonded}} + |
79 |
|
|
\underbrace{V_{\text{LJ}} + V_{\text{Dp}} + % |
80 |
|
|
V_{\text{SSD}}}_{\text{non-bonded}} \label{eq:totalPotential} |
81 |
|
|
\end{equation} |
82 |
mmeineke |
666 |
|
83 |
mmeineke |
698 |
\subsection{Bonded Interactions} |
84 |
|
|
\label{subSec:bondedInteractions} |
85 |
mmeineke |
664 |
|
86 |
mmeineke |
698 |
The bonded interactions in the DUFF functional set are limited to the |
87 |
|
|
bend potential and the torsional potential. Bond potentials are not |
88 |
|
|
calculated, instead all bond lengths are fixed to allow for large time |
89 |
|
|
steps to be taken between force evaluations. |
90 |
mmeineke |
666 |
|
91 |
mmeineke |
698 |
The bend functional is of the form: |
92 |
|
|
\begin{equation} |
93 |
|
|
V_{\theta} = \sum k_{\theta}( \theta - \theta_0 )^2 \label{eq:bendPot} |
94 |
|
|
\end{equation} |
95 |
|
|
$k_{\theta}$, the force constant, and $\theta_0$, the equilibrium bend |
96 |
|
|
angle, were taken from the TraPPE forcefield of Siepmann. |
97 |
|
|
|
98 |
|
|
The torsion functional has the form: |
99 |
|
|
\begin{equation} |
100 |
mmeineke |
709 |
V_{\phi} = \sum ( k_3 \cos^3 \phi + k_2 \cos^2 \phi + k_1 \cos \phi + k_0) |
101 |
mmeineke |
698 |
\label{eq:torsionPot} |
102 |
|
|
\end{equation} |
103 |
|
|
Here, the authors decided to use a potential in terms of a power |
104 |
|
|
expansion in $\cos \phi$ rather than the typical expansion in |
105 |
|
|
$\phi$. This prevents the need for repeated trigonemtric |
106 |
|
|
evaluations. Again, all $k_n$ constants were based on those in TraPPE. |
107 |
|
|
|
108 |
|
|
\subsection{Non-Bonded Interactions} |
109 |
|
|
\label{subSec:nonBondedInteractions} |
110 |
|
|
|
111 |
|
|
\begin{equation} |
112 |
|
|
V_{\text{LJ}} = \text{internal + external} |
113 |
|
|
\end{equation} |
114 |
|
|
|
115 |
|
|
|