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\section{\label{sec:empericalEnergy}The Emperical Energy Functions} |
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\section{\label{sec:empiricalEnergy}The Empirical Energy Functions} |
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\subsection{\label{sec:atomsMolecules}Atoms, Molecules and Rigid Bodies} |
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The basic unit of an {\sc oopse} simulation is the atom. The parameters |
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describing the atom are generalized to make the atom as flexible a |
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representation as possible. They may represent specific atoms of an |
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element, or be used for collections of atoms such as a methyl |
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group. The atoms are also capable of having a directional component |
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associated with them, often in the form of a dipole. Charges on atoms |
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are not currently suported by {\sc oopse}. |
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The basic unit of an {\sc oopse} simulation is the atom. The |
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parameters describing the atom are generalized to make the atom as |
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flexible a representation as possible. They may represent specific |
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atoms of an element, or be used for collections of atoms such as |
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methyl and carbonyl groups. The atoms are also capable of having |
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directional components associated with them (\emph{e.g.}~permanent |
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dipoles). Charges on atoms are not currently supported by {\sc oopse}. |
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\begin{lstlisting}[caption={[Specifier for molecules and atoms] An example specifing the simple Ar molecule},label=sch:AtmMole] |
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\begin{lstlisting}[caption={[Specifier for molecules and atoms] An example specifying the simple Ar molecule},label=sch:AtmMole] |
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molecule{ |
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name = "Ar"; |
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nAtoms = 1; |
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\subsection{\label{sec:LJPot}The Lennard Jones Potential} |
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The most basic force field implemented in OOPSE is the Lennard-Jones |
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The most basic force field implemented in {\sc oopse} is the Lennard-Jones |
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potential. The Lennard-Jones potential. Which mimics the Van der Waals |
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interaction at long distances, and uses an emperical repulsion at |
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interaction at long distances, and uses an empirical repulsion at |
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short distances. The Lennard-Jones potential is given by: |
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\begin{equation} |
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V_{\text{LJ}}(r_{ij}) = |
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Because this potential is calculated between all pairs, the force |
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evaluation can become computationally expensive for large systems. To |
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keep the pair evaluation to a manegable number, OOPSE employs a |
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keep the pair evaluation to a manageable number, {\sc oopse} employs a |
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cut-off radius.\cite{allen87:csl} The cutoff radius is set to be |
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$2.5\sigma_{ii}$, where $\sigma_{ii}$ is the largest Lennard-Jones length |
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parameter in the system. Truncating the calculation at |
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phosphatidylcholine.\cite{Cevc87} Additionally, a Lennard-Jones site |
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is located at the pseudoatom's center of mass. The model is |
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illustrated by the dark grey atom in Fig.~\ref{fig:lipidModel}. The water model we use to complement the dipoles of the lipids is out |
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repaarameterization of the soft sticky dipole (SSD) model of Ichiye |
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reparameterization of the soft sticky dipole (SSD) model of Ichiye |
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\emph{et al.}\cite{liu96:new_model} |
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\begin{figure} |
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\end{equation} |
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Here $\phi_{ijkl}$ is the angle defined by four bonded neighbors $i$, |
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$j$, $k$, and $l$ (again, see Fig.~\ref{fig:lipidModel}). For |
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computaional efficency, the torsion potential has been recast after |
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computational efficiency, the torsion potential has been recast after |
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the method of CHARMM\cite{charmm1983} whereby the angle series is |
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converted to a power series of the form: |
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\begin{equation} |
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$\boldsymbol{\Omega}_i$. |
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\subsection{\label{sec:SSD}The {\sc DUFF} Water Models: SSD/E and SSD/RF} |
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\subsection{\label{sec:SSD}The {\sc duff} Water Models: SSD/E and SSD/RF} |
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In the interest of computational efficiency, the default solvent used |
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by {\sc oopse} is the extended Soft Sticky Dipole (SSD/E) water |
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describes the interaction of the positively charged metal core ions |
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with one another. A particular potential description called the |
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Embedded Atom Method\cite{Daw84,FBD86,johnson89,Lu97}({\sc eam}) that has |
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particularly wide adoption has been selected for inclusion in OOPSE. A |
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particularly wide adoption has been selected for inclusion in {\sc oopse}. A |
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good review of {\sc eam} and other metallic potential formulations was done |
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by Voter.\cite{voter} |
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where $F_{i} $ is the embedding function that equates the energy required to embed a |
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positively-charged core ion $i$ into a linear superposition of |
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sperically averaged atomic electron densities given by |
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spherically averaged atomic electron densities given by |
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$\rho_{i}$. $\phi_{ij}$ is a primarily repulsive pairwise interaction |
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between atoms $i$ and $j$. In the original formulation of |
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{\sc eam} cite{Daw84}, $\phi_{ij}$ was an entirely repulsive term, however |
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simulation box is large enough to avoid "feeling" the symmetries of |
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the periodic lattice, surface effects can be ignored. Cubic, |
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orthorhombic and parallelepiped are the available periodic cells In |
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OOPSE. We use a matrix to describe the property of the simulation |
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{\sc oopse}. We use a matrix to describe the property of the simulation |
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box. Therefore, both the size and shape of the simulation box can be |
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changed during the simulation. The transformation from box space |
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vector $\mathbf{s}$ to its corresponding real space vector |
