\documentclass[a4paper, english, 10pt]{article}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}
\usepackage[left=20mm,right=20mm,top=15mm,bottom=10mm]{geometry}
\usepackage{pslatex}
\usepackage{float}
\usepackage{graphicx}
\usepackage{color}
\usepackage{subcaption}
\usepackage{amsmath}
\usepackage{pgfplots}
\usepackage{pgfplotstable}
\usepackage{hyperref}
% System colors
\definecolor{POPC}{RGB}{228,26,28}
\definecolor{DPPC}{RGB}{55,126,184}
\definecolor{CERA}{RGB}{77,175,74}
\definecolor{SM16}{RGB}{152,78,163}
\definecolor{LB2R}{RGB}{255,127,0}
\definecolor{LB14}{RGB}{255,255,51}
\definecolor{LB16}{RGB}{139,69,19}
\pgfplotscreateplotcyclelist{System}{%
POPC\\%
DPPC\\%
CERA\\%
SM16\\%
LB2R\\%
LB14\\%
LB16\\%
}
% 5 Colors
\pgfplotscreateplotcyclelist{5colors}{%
red!0!yellow\\%
red!25!yellow\\%
red!50!yellow\\%
red!75!yellow\\%
red!100!yellow\\%
}
% external tikz
\usetikzlibrary{external}
\tikzexternalize[prefix=tikz/]
\tikzset{external/up to date check=md5}
% header
\pagestyle{headings}
% compact lists
\usepackage{enumitem}
\setlist[itemize]{noitemsep}
% Function for drawing plots with errorbands
\usepgfplotslibrary{fillbetween}
\newcommand{\errorband}[2][solid]{
\addplot+[name path=pluserror,draw=none,no markers,forget plot]
table [comment chars={@,\#}, x index=0,y expr=\thisrowno{1}+\thisrowno{2}] {#2};
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table [comment chars={@,\#}, x index=0,y expr=\thisrowno{1}-\thisrowno{2}] {#2};
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fill between[on layer={},of=pluserror and minuserror];
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select row/.style={
x filter/.code={\ifnum\coordindex=#1\else\def\pgfmathresult{}\fi}
}
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% global pgfplots settings
\pgfplotsset{
/pgfplots/table/comment chars={@,\#}, % read XVG files with pgfplots
%width=3.33in, height=3.33in,
every axis plot/.append style={line width=1.5pt},
/pgfplots/error bars/error bar style={line width=1.5pt},
/pgfplots/error bars/error mark options={rotate=90, line width=1.5pt, mark size=3pt},
width=12cm, height=9cm,
legend style={at={(1,1)},anchor=north west},
legend cell align=left,
cycle multi list={System},
legend style={font=\footnotesize},
}
\begin{document}
\title{\LARGE Role of lipids in endosomal/lysosomal cholesterol transport}
\author{Heikki Mikkolainen}
\maketitle
\tableofcontents
\clearpage
\section{Simulations}
\begin{itemize}
\item{100 lipids (50 per leaflet), 10\% cholesterol and 30\% DPPC/CERA/SM16/LBPA}
\begin{table}[H]
\begin{tabular}{l|c|c}
system & NPT simulation [ns] & FEP simulation [ns] \\ \hline
90 POPC + 10 CHOL & 500 & 100+100 \\
60 POPC + 10 CHOL + 30 DPPC & 500 & 101+100+100+100 \\
60 POPC + 10 CHOL + 30 CERA & 500 & 100+100 \\
60 POPC + 10 CHOL + 30 SM16 & 500 & 101+100 \\
60 POPC + 10 CHOL + 30 LBPA$_{\text{18:1}}$ & 500 & 103+100 \\
60 POPC + 10 CHOL + 30 LBPA$_{\text{16:0}}$ & 500 & 100+100 \\
60 POPC + 10 CHOL + 30 LBPA$_{\text{14:0}}$ & 500 & 100+100 \\
\end{tabular}
\end{table}
\end{itemize}
\subsubsection*{Old test simulations, results not shown here}
\begin{itemize}
\item{Small membranes, 100 lipids (50 per leaflet), 10\% cholesterol and 16\% LBPA}
\begin{table}[H]
\begin{tabular}{l|c|c}
system & NPT simulation [ns] & FEP simulation [ns] \\ \hline
74 POPC + 10 CHOL + 16 LBPA$_{\text{RR}}$ &200& \\
74 POPC + 10 CHOL + 16 LBPA$_{\text{SS}}$ &200& \\
\end{tabular}
\end{table}
\item{Big membranes, 200 lipids (100 per leaflet), 10\% cholesterol and 15\% CERA/SM16/LBPA}
\begin{table}[H]
\begin{tabular}{l|c|c}
system & NPT simulation [ns] & FEP simulation [ns] \\ \hline
180 POPC + 20 CHOL &200 &23 \\
150 POPC + 20 CHOL + 30 CERA &200 &20 \\
150 POPC + 20 CHOL + 30 SM16 &200 &11 \\
150 POPC + 20 CHOL + 30 LBPA$_{\text{RR}}$ &200 &17 \\
150 POPC + 20 CHOL + 30 LBPA$_{\text{SS}}$ &200 &23 \\
\end{tabular}
\end{table}
\item{Big membranes, 200 lipids (100 per leaflet), 10\% cholesterol and 90\% CERA/SM16}
\begin{table}[H]
\begin{tabular}{l|c|c}
system & NPT simulation [ns] & FEP simulation [ns] \\ \hline
180 CERA + 20 CHOL &200 &18 \\
180 SM16 + 20 CHOL &200 &20 \\
\end{tabular}
\end{table}
\item{Big membranes, 200 lipids (100 per leaflet), 0.5 \% cholesterol}
\begin{table}[H]
\begin{tabular}{l|c|c}
system & NPT simulation [ns] & FEP simulation [ns] \\ \hline
199 POPC + 1 CHOL &200 &17 \\
169 POPC + 1 CHOL + 30 CERA &200 &18 \\
169 POPC + 1 CHOL + 30 SM16 &200 &24 \\
169 POPC + 1 CHOL + 30 LBPA$_{\text{RR}}$ &200 &18 \\
169 POPC + 1 CHOL + 30 LBPA$_{\text{SS}}$ &200 &24
\end{tabular}
\end{table}
\end{itemize}
\clearpage
\section{Results}
\subsection{Membrane area}
\pgfplotsset{membrane_area/.style={
height=7.5cm,
xmin=0, xmax=200000,
xlabel={time [ns]},
scaled x ticks={real:1000},
xtick scale label code/.code={},
ylabel={ xy-area [nm$^2$]},
table/x index=0,
table/y expr=\thisrowno{1} * \thisrowno{2} / 100,
}}
\begin{figure}[H]
\centering
\tikzsetnextfilename{box}
\begin{tikzpicture}
\begin{axis}[membrane_area, xmax=500000, table/y expr=\thisrowno{1} * \thisrowno{2} / 50,]
\addplot table {data/90POPC_10CHOL/analys/box/box_500-mean.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/box/box_500-mean.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/box/box_500-mean.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/box/box_500-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/box/box_500-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/box/box_50-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/box/box_50-mean.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Area per lipid. }}
\end{figure}
\pgfplotsset{sasa/.style={
height=7.5cm,
xmin=0, xmax=200000,
xlabel={time [ns]},
scaled x ticks={real:1000},
xtick scale label code/.code={},
ylabel={SASA [nm$^2$]},
table/x index=0,
table/y index=2,
}}
\begin{figure}[H]
\centering
\tikzsetnextfilename{sasa}
\begin{tikzpicture}
\begin{axis}[sasa, xmax=500000]
\addplot table {data/90POPC_10CHOL/analys/sas/Membrane-area_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/sas/Membrane-area_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/sas/Membrane-area_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/sas/Membrane-area_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/sas/Membrane-area_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/sas/Membrane-area_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/sas/Membrane-area_20-mean.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf Solvent accessible surface area (SASA) of membrane. }}
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{sasa_CHOL}
\begin{tikzpicture}
\begin{axis}[sasa, xmax=500000]
\addplot table {data/90POPC_10CHOL/analys/sas/CHOL-area_50-mean.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/sas/CHOL-area_50-mean.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/sas/CHOL-area_50-mean.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/sas/CHOL-area_50-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/sas/CHOL-area_50-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/sas/CHOL-area_50-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/sas/CHOL-area_50-mean.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf Solvent accessible surface area (SASA) of cholesterol. }}
\end{figure}
\clearpage
\subsection{Atom distance from bilayer center}
\pgfplotsset{z_distance/.style={
height=8.0cm,
xmin=0, xmax=200000,
xlabel={time [ns]},
scaled x ticks={real:1000},
xtick scale label code/.code={},
ylabel={z-distance [nm]},
minor y tick num=1,
}}
\begin{figure}[H]
\centering
\tikzsetnextfilename{dist_P}
\begin{tikzpicture}
\begin{axis}[z_distance,xmax=500000]
\addplot table {data/90POPC_10CHOL/analys/dist/POPC_P/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/dist/POPC_P/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/dist/POPC_P/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/dist/POPC_P/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/dist/POPC_P/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/dist/POPC_P/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/dist/POPC_P/absz_average_20-mean.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Absolute distance of POPC Phosphate from bilayer center. } }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{dist_CHOL}
\begin{tikzpicture}
\begin{axis}[z_distance,xmax=500000]
\addplot table {data/90POPC_10CHOL/analys/dist/CHOL/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/dist/CHOL/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/dist/CHOL/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/dist/CHOL/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL/absz_average_20-mean.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Absolute distance of cholesterol COM from bilayer center. } }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{dist_CHOLC3}
\begin{tikzpicture}
\begin{axis}[z_distance,xmax=500000]
\addplot table {data/90POPC_10CHOL/analys/dist/CHOL_C3/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C3/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C3/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C3/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C3/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C3/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C3/absz_average_20-mean.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Absolute distance of cholesterol C3 atom from bilayer center. } }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{dist_CHOLC17}
\begin{tikzpicture}
\begin{axis}[z_distance,xmax=500000]
\addplot table {data/90POPC_10CHOL/analys/dist/CHOL_C17/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C17/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C17/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C17/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C17/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C17/absz_average_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C17/absz_average_20-mean.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Absolute distance of cholesterol C17 atom from bilayer center. } }
\end{figure}
\subsection{Flip flops}
\begin{figure}[H]
\centering
\tikzsetnextfilename{distance_POPC}
\begin{tikzpicture}
\begin{axis}[z_distance,xmax=500000]
\addplot [red] table [y index=1]{data/90POPC_10CHOL/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=2]{data/90POPC_10CHOL/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=3]{data/90POPC_10CHOL/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=4]{data/90POPC_10CHOL/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=5]{data/90POPC_10CHOL/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=6]{data/90POPC_10CHOL/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=7]{data/90POPC_10CHOL/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=8]{data/90POPC_10CHOL/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=9]{data/90POPC_10CHOL/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=10]{data/90POPC_10CHOL/analys/dist/CHOL_C3/z_20-mean.xvg};
\end{axis}
\end{tikzpicture}
\caption{{\bf Distances of all cholesterol C3 atoms from bilayer center. 90POPC\_10CHOL} }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{distance_DPPC}
\begin{tikzpicture}
\begin{axis}[z_distance,xmax=500000]
\addplot [red] table [y index=1]{data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=2]{data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=3]{data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=4]{data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=5]{data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=6]{data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=7]{data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=8]{data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=9]{data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=10]{data/60POPC_10CHOL_30DPPC/analys/dist/CHOL_C3/z_20-mean.xvg};
\end{axis}
\end{tikzpicture}
\caption{{\bf Distances of all cholesterol C3 atoms from bilayer center. 60POPC\_10CHOL\_DPPC} }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{distance_CERA}
\begin{tikzpicture}
\begin{axis}[z_distance,xmax=500000]
\addplot [red] table [y index=1]{data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=2]{data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=3]{data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=4]{data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=5]{data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=6]{data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=7]{data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=8]{data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=9]{data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=10]{data/60POPC_10CHOL_30CERA/analys/dist/CHOL_C3/z_20-mean.xvg};
\end{axis}
\end{tikzpicture}
\caption{{\bf Distances of all cholesterol C3 atoms from bilayer center. 60POPC\_10CHOL\_CERA} }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{distance_SM16}
\begin{tikzpicture}
\begin{axis}[z_distance,xmax=500000]
\addplot [red] table [y index=1]{data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=2]{data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=3]{data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=4]{data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=5]{data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=6]{data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=7]{data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=8]{data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=9]{data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=10]{data/60POPC_10CHOL_30SM16/analys/dist/CHOL_C3/z_20-mean.xvg};
\end{axis}
\end{tikzpicture}
\caption{{\bf Distances of all cholesterol C3 atoms from bilayer center. 60POPC\_10CHOL\_SM16} }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{distance_LBPA22RR}
\begin{tikzpicture}
\begin{axis}[z_distance,xmax=500000]
\addplot [red] table [y index=1]{data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=2]{data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=3]{data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=4]{data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=5]{data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=6]{data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=7]{data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=8]{data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=9]{data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=10]{data/60POPC_10CHOL_30LBPA22RR/analys/dist/CHOL_C3/z_20-mean.xvg};
\end{axis}
\end{tikzpicture}
\caption{{\bf Distances of all cholesterol C3 atoms from bilayer center. 60POPC\_10CHOL\_LBPA$_\text{18:1}$} }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{distance_LBPA14}
\begin{tikzpicture}
\begin{axis}[z_distance,xmax=500000]
\addplot [red] table [y index=1]{data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=2]{data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=3]{data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=4]{data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=5]{data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=6]{data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=7]{data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=8]{data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=9]{data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=10]{data/60POPC_10CHOL_30LBPA14/analys/dist/CHOL_C3/z_20-mean.xvg};
\end{axis}
\end{tikzpicture}
\caption{{\bf Distances of all cholesterol C3 atoms from bilayer center. 60POPC\_10CHOL\_LBPA$_\text{14:0}$} }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{distance_LBPA16}
\begin{tikzpicture}
\begin{axis}[z_distance,xmax=500000]
\addplot [red] table [y index=1]{data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=2]{data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=3]{data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=4]{data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [red] table [y index=5]{data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=6]{data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=7]{data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=8]{data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=9]{data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C3/z_20-mean.xvg};
\addplot [blue] table [y index=10]{data/60POPC_10CHOL_30LBPA16/analys/dist/CHOL_C3/z_20-mean.xvg};
\end{axis}
\end{tikzpicture}
\caption{{\bf Distances of all cholesterol C3 atoms from bilayer center. 60POPC\_10CHOL\_LBPA$_\text{16:0}$} }
\end{figure}
\clearpage
\subsection{Order parameter}
\pgfplotsset{order/.style={
xmin=1, xmax=18,
ymin=0, ymax=0.35,
width=8.5cm,
height=9cm,
yticklabel style={/pgf/number format/fixed,
/pgf/number format/fixed zerofill,
/pgf/number format/precision=2},
xlabel={atom},
ylabel={S$_{\text{CD}}$},
table/y error plus index = 2,
table/y error minus index = 2,
error bars/y dir=both,
error bars/y explicit,
legend columns=2,
legend style={at={(0,1.05)},anchor=south west},
transpose legend,
}}
\begin{figure}[H]
\begin{subfigure}[b]{0.49\textwidth}
\centering
\tikzsetnextfilename{POPCsn1_order}
\begin{tikzpicture}
\begin{axis}[order]
\addplot table {data/90POPC_10CHOL/analys/order_b50000/POPC_SN1/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/order_b50000/POPC_SN1/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/order_b50000/POPC_SN1/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/order_b50000/POPC_SN1/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/order_b50000/POPC_SN1/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/order_b50000/POPC_SN1/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/order_b50000/POPC_SN1/50001-500000_deuter_fixed.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{SN1-palmitoyl}
\end{subfigure}
\begin{subfigure}[b]{0.49\textwidth}
\centering
\tikzsetnextfilename{POPCsn2_order}
\begin{tikzpicture}
\begin{axis}[order, ylabel={}, yticklabels={,,},]
\addplot table {data/90POPC_10CHOL/analys/order_b50000/POPC_SN2/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/order_b50000/POPC_SN2/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/order_b50000/POPC_SN2/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/order_b50000/POPC_SN2/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/order_b50000/POPC_SN2/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/order_b50000/POPC_SN2/50001-500000_deuter_fixed.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/order_b50000/POPC_SN2/50001-500000_deuter_fixed.xvg};
\end{axis}
\end{tikzpicture}
\caption{SN2-oleyl}
\end{subfigure}
\caption{ {\bf POPC tail deuterium order parameters. } }
\end{figure}
\begin{figure}[H]
\begin{subfigure}[b]{0.49\textwidth}
\centering
\tikzsetnextfilename{DPPCsn1_order}
\begin{tikzpicture}
\begin{axis}[order]
\addplot [DPPC] table {data/60POPC_10CHOL_30DPPC/analys/order_b50000/DPPC_SN1/50001-500000_deuter_fixed.xvg};
\addplot [CERA] table {data/60POPC_10CHOL_30CERA/analys/order_b50000/CERA_1/50001-500000_deuter_fixed.xvg};
\addplot [SM16] table {data/60POPC_10CHOL_30SM16/analys/order_b50000/SM16_1/50001-500000_deuter_fixed.xvg};
\addplot [LB2R] table {data/60POPC_10CHOL_30LBPA22RR/analys/order_b50000/LBPA_1/50001-500000_deuter_fixed.xvg};
\addplot [LB14] table {data/60POPC_10CHOL_30LBPA14/analys/order_b50000/LBPA14_1/50001-500000_deuter_fixed.xvg};
\addplot [LB16] table {data/60POPC_10CHOL_30LBPA16/analys/order_b50000/LBPA16_1/50001-500000_deuter_fixed.xvg};
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{DPPC SN1, CERA/SM16 sphingosine, LBPA tail 1}
\end{subfigure}
\begin{subfigure}[b]{0.49\textwidth}
\centering
\tikzsetnextfilename{DPPCsn2_order}
\begin{tikzpicture}
\begin{axis}[order, ylabel={}, yticklabels={,,},]
\addplot [DPPC] table {data/60POPC_10CHOL_30DPPC/analys/order_b50000/DPPC_SN2/50001-500000_deuter_fixed.xvg};
\addplot [CERA] table {data/60POPC_10CHOL_30CERA/analys/order_b50000/CERA_2/50001-500000_deuter_fixed.xvg};
\addplot [SM16] table {data/60POPC_10CHOL_30SM16/analys/order_b50000/SM16_2/50001-500000_deuter_fixed.xvg};
\addplot [LB2R] table {data/60POPC_10CHOL_30LBPA22RR/analys/order_b50000/LBPA_2/50001-500000_deuter_fixed.xvg};
\addplot [LB14] table {data/60POPC_10CHOL_30LBPA14/analys/order_b50000/LBPA14_2/50001-500000_deuter_fixed.xvg};
\addplot [LB16] table {data/60POPC_10CHOL_30LBPA16/analys/order_b50000/LBPA16_2/50001-500000_deuter_fixed.xvg};
\end{axis}
\end{tikzpicture}
\caption{DPPC SN2, CERA/SM16 palmitoyl, LBPA tail 2}
\end{subfigure}
\caption{ {\bf DPPC/CERA/SM16/LBPA tail deuterium order parameters. }}
\end{figure}
\clearpage
\pgfplotsset{density/.style={
xmin=-2.5, xmax=2.5,
height=7.5cm,
ymin=0,
minor x tick num={4},
xlabel={z [nm]},
ylabel={density [nm$^{-3}$]},
}}
\subsection{Cholesterol density}
\begin{figure}[H]
\begin{subfigure}[b]{\textwidth}
\centering
\tikzsetnextfilename{CHOL_density}
\begin{tikzpicture}
\begin{axis}[density]
\errorband {data/90POPC_10CHOL/analys/density_b50000/CHOL/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30DPPC/analys/density_b50000/CHOL/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30CERA/analys/density_b50000/CHOL/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30SM16/analys/density_b50000/CHOL/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30LBPA22RR/analys/density_b50000/CHOL/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30LBPA14/analys/density_b50000/CHOL/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30LBPA16/analys/density_b50000/CHOL/50001-500000_density_sl250_number.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ All cholesterol atoms}
\end{subfigure}
\begin{subfigure}[b]{\textwidth}
\centering
\tikzsetnextfilename{CHOL_C3_density}
\begin{tikzpicture}
\begin{axis}[density]
\errorband {data/90POPC_10CHOL/analys/density_b50000/CHOL_C3/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30DPPC/analys/density_b50000/CHOL_C3/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30CERA/analys/density_b50000/CHOL_C3/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30SM16/analys/density_b50000/CHOL_C3/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30LBPA22RR/analys/density_b50000/CHOL_C3/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30LBPA14/analys/density_b50000/CHOL_C3/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30LBPA16/analys/density_b50000/CHOL_C3/50001-500000_density_sl250_number.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ Cholesterol C3-atoms.}
\end{subfigure}
\begin{subfigure}[b]{\textwidth}
\centering
\tikzsetnextfilename{CHOL_C17_density}
\begin{tikzpicture}
\begin{axis}[density]
\errorband {data/90POPC_10CHOL/analys/density_b50000/CHOL_C17/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30DPPC/analys/density_b50000/CHOL_C17/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30CERA/analys/density_b50000/CHOL_C17/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30SM16/analys/density_b50000/CHOL_C17/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30LBPA22RR/analys/density_b50000/CHOL_C17/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30LBPA14/analys/density_b50000/CHOL_C17/50001-500000_density_sl250_number.xvg};
\errorband {data/60POPC_10CHOL_30LBPA16/analys/density_b50000/CHOL_C17/50001-500000_density_sl250_number.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ Cholesterol C17-atoms.}
\end{subfigure}
\caption{ {\bf Number density of cholesterol atoms through membrane.} }
\end{figure}
\clearpage
\subsection{RDF of lipids around cholesterol}
\pgfplotsset{rdf/.style={
height=8.5cm,
width=\textwidth,
xlabel={r [nm]},
ylabel={g($r$)},
xmin=0,
xmax=3.5,
legend columns=2,
legend style={at={(0,1.05)},anchor=south west},
transpose legend,
}}
\begin{figure}[H]
\begin{subfigure}[b]{0.50\textwidth}
\centering
\tikzsetnextfilename{rdf_POPC_A}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband {data/90POPC_10CHOL/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30DPPC/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30CERA/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30SM16/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30LBPA22RR/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30LBPA14/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30LBPA16/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_A.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Leaflet A }}
\end{subfigure}
\begin{subfigure}[b]{0.50\textwidth}
\centering
\tikzsetnextfilename{rdf_POPC_B}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband {data/90POPC_10CHOL/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30DPPC/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30CERA/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30SM16/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30LBPA22RR/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30LBPA14/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30LBPA16/analys/rdf_b50000/POPC/50001-500000_rdf_leaflet_B.xvg};
\end{axis}
\end{tikzpicture}
\caption{{\bf Leaflet B }}
\end{subfigure}
\caption{{\bf Radial distribution function (RDF) of POPC around cholesterol. } }
\end{figure}
\begin{figure}[H]
\begin{subfigure}[b]{0.50\textwidth}
\centering
\tikzsetnextfilename{rdf_DPPC_A}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband [DPPC] {data/60POPC_10CHOL_30DPPC/analys/rdf_b50000/DPPC/50001-500000_rdf_leaflet_A.xvg};
\errorband [CERA] {data/60POPC_10CHOL_30CERA/analys/rdf_b50000/CERA/50001-500000_rdf_leaflet_A.xvg};
\errorband [SM16] {data/60POPC_10CHOL_30SM16/analys/rdf_b50000/SM16/50001-500000_rdf_leaflet_A.xvg};
\errorband [LB2R] {data/60POPC_10CHOL_30LBPA22RR/analys/rdf_b50000/LBPA/50001-500000_rdf_leaflet_A.xvg};
\errorband [LB14] {data/60POPC_10CHOL_30LBPA14/analys/rdf_b50000/LBPA/50001-500000_rdf_leaflet_A.xvg};
\errorband [LB16] {data/60POPC_10CHOL_30LBPA16/analys/rdf_b50000/LBPA/50001-500000_rdf_leaflet_A.xvg};
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Leaflet A }}
\end{subfigure}
\begin{subfigure}[b]{0.50\textwidth}
\tikzsetnextfilename{rdf_DPPC_B}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband [DPPC] {data/60POPC_10CHOL_30DPPC/analys/rdf_b50000/DPPC/50001-500000_rdf_leaflet_B.xvg};
\errorband [CERA] {data/60POPC_10CHOL_30CERA/analys/rdf_b50000/CERA/50001-500000_rdf_leaflet_B.xvg};
\errorband [SM16] {data/60POPC_10CHOL_30SM16/analys/rdf_b50000/SM16/50001-500000_rdf_leaflet_B.xvg};
\errorband [LB2R] {data/60POPC_10CHOL_30LBPA22RR/analys/rdf_b50000/LBPA/50001-500000_rdf_leaflet_B.xvg};
\errorband [LB14] {data/60POPC_10CHOL_30LBPA14/analys/rdf_b50000/LBPA/50001-500000_rdf_leaflet_B.xvg};
\errorband [LB16] {data/60POPC_10CHOL_30LBPA16/analys/rdf_b50000/LBPA/50001-500000_rdf_leaflet_B.xvg};
\end{axis}
\end{tikzpicture}
\caption{{\bf Leaflet B }}
\end{subfigure}
\caption{{\bf Radial distribution function (RDF) of DPPC/CERA/SM16/LBPA around cholesterol. } }
\end{figure}
\begin{figure}[H]
\begin{subfigure}[b]{0.50\textwidth}
\centering
\tikzsetnextfilename{rdffep_POPC_A}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband {data/90POPC_10CHOL/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30CERA/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30SM16/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{Leaflet A (FEP-simulation leaflet A)}
\end{subfigure}
\begin{subfigure}[b]{0.50\textwidth}
\tikzsetnextfilename{rdffep_POPC_B}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband {data/90POPC_10CHOL/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30CERA/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30SM16/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_A/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\end{axis}
\end{tikzpicture}
\caption{Leaflet B (FEP-simulation leaflet A)}
\end{subfigure}
\begin{subfigure}[b]{0.50\textwidth}
\centering
\tikzsetnextfilename{rdffep_POPC_A_rep2}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband {data/90POPC_10CHOL/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30CERA/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30SM16/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\errorband {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_A.xvg};
\end{axis}
\end{tikzpicture}
\caption{Leaflet A (FEP-simulation leaflet B)}
\end{subfigure}
\begin{subfigure}[b]{0.50\textwidth}
\tikzsetnextfilename{rdffep_POPC_B_rep2}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband {data/90POPC_10CHOL/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30CERA/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30SM16/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\errorband {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_B/analys/rdf_b10000/POPC/1-100000_rdf_leaflet_B.xvg};
\end{axis}
\end{tikzpicture}
\caption{Leaflet B (FEP-simulation leaflet B)}
\end{subfigure}
\caption{{\bf Radial distribution function (RDF) of POPC around cholesterol. Calculated from FEP simulations (lambda0). } }
\end{figure}
\begin{figure}[H]
\begin{subfigure}[b]{0.50\textwidth}
\centering
\tikzsetnextfilename{rdffep_DPPC_A}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband [DPPC] {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_A/analys/rdf_b10000/DPPC/1-100000_rdf_leaflet_A.xvg};
\errorband [CERA] {data/60POPC_10CHOL_30CERA/free_energy/leaflet_A/analys/rdf_b10000/CERA/1-100000_rdf_leaflet_A.xvg};
\errorband [SM16] {data/60POPC_10CHOL_30SM16/free_energy/leaflet_A/analys/rdf_b10000/SM16/1-100000_rdf_leaflet_A.xvg};
\errorband [LB2R] {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_A/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_A.xvg};
\errorband [LB14] {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_A/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_A.xvg};
\errorband [LB16] {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_A/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_A.xvg};
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{Leaflet A (FEP-simulation leaflet A)}
\end{subfigure}
\begin{subfigure}[b]{0.50\textwidth}
\tikzsetnextfilename{rdffep_DPPC_B}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband [DPPC] {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_A/analys/rdf_b10000/DPPC/1-100000_rdf_leaflet_B.xvg};
\errorband [CERA] {data/60POPC_10CHOL_30CERA/free_energy/leaflet_A/analys/rdf_b10000/CERA/1-100000_rdf_leaflet_B.xvg};
\errorband [SM16] {data/60POPC_10CHOL_30SM16/free_energy/leaflet_A/analys/rdf_b10000/SM16/1-100000_rdf_leaflet_B.xvg};
\errorband [LB2R] {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_A/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_B.xvg};
\errorband [LB14] {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_A/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_B.xvg};
\errorband [LB16] {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_A/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_B.xvg};
\end{axis}
\end{tikzpicture}
\caption{Leaflet B (FEP-simulation leaflet A)}
\end{subfigure}
\begin{subfigure}[b]{0.50\textwidth}
\centering
\tikzsetnextfilename{rdffep_DPPC_A_rep2}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband [DPPC] {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_B/analys/rdf_b10000/DPPC/1-100000_rdf_leaflet_A.xvg};
\errorband [CERA] {data/60POPC_10CHOL_30CERA/free_energy/leaflet_B/analys/rdf_b10000/CERA/1-100000_rdf_leaflet_A.xvg};
\errorband [SM16] {data/60POPC_10CHOL_30SM16/free_energy/leaflet_B/analys/rdf_b10000/SM16/1-100000_rdf_leaflet_A.xvg};
\errorband [LB2R] {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_B/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_A.xvg};
\errorband [LB14] {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_B/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_A.xvg};
\errorband [LB16] {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_B/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_A.xvg};
\end{axis}
\end{tikzpicture}
\caption{Leaflet A (FEP-simulation leaflet B)}
\end{subfigure}
\begin{subfigure}[b]{0.50\textwidth}
\tikzsetnextfilename{rdffep_DPPC_B_rep2}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband [DPPC] {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_B/analys/rdf_b10000/DPPC/1-100000_rdf_leaflet_B.xvg};
\errorband [CERA] {data/60POPC_10CHOL_30CERA/free_energy/leaflet_B/analys/rdf_b10000/CERA/1-100000_rdf_leaflet_B.xvg};
\errorband [SM16] {data/60POPC_10CHOL_30SM16/free_energy/leaflet_B/analys/rdf_b10000/SM16/1-100000_rdf_leaflet_B.xvg};
\errorband [LB2R] {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_B/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_B.xvg};
\errorband [LB14] {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_B/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_B.xvg};
\errorband [LB16] {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_B/analys/rdf_b10000/LBPA/1-100000_rdf_leaflet_B.xvg};
\end{axis}
\end{tikzpicture}
\caption{Leaflet B (FEP-simulation leaflet B)}
\end{subfigure}
\caption{{\bf Radial distribution function (RDF) of DPPC/CERA/SM16/LBPA around cholesterol. Calculated from FEP simulations (lambda0). } }
\end{figure}
\begin{figure}[H]
\begin{subfigure}[b]{0.50\textwidth}
\centering
\tikzsetnextfilename{average_rdf_POPC}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband {data/90POPC_10CHOL/analys/average_rdf_POPC.xvg};
\errorband {data/60POPC_10CHOL_30DPPC/analys/average_rdf_POPC.xvg};
\errorband {data/60POPC_10CHOL_30CERA/analys/average_rdf_POPC.xvg};
\errorband {data/60POPC_10CHOL_30SM16/analys/average_rdf_POPC.xvg};
\errorband {data/60POPC_10CHOL_30LBPA22RR/analys/average_rdf_POPC.xvg};
\errorband {data/60POPC_10CHOL_30LBPA14/analys/average_rdf_POPC.xvg};
\errorband {data/60POPC_10CHOL_30LBPA16/analys/average_rdf_POPC.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{POPC}
\end{subfigure}
\begin{subfigure}[b]{0.50\textwidth}
\centering
\tikzsetnextfilename{average_rdf_DPPC}
\begin{tikzpicture}
\begin{axis}[rdf, xmax=2.5]
\errorband [DPPC] {data/60POPC_10CHOL_30DPPC/analys/average_rdf_DPPC.xvg};
\errorband [CERA] {data/60POPC_10CHOL_30CERA/analys/average_rdf_CERA.xvg};
\errorband [SM16] {data/60POPC_10CHOL_30SM16/analys/average_rdf_SM16.xvg};
\errorband [LB2R] {data/60POPC_10CHOL_30LBPA22RR/analys/average_rdf_LBPA.xvg};
\errorband [LB14] {data/60POPC_10CHOL_30LBPA14/analys/average_rdf_LBPA.xvg};
\errorband [LB16] {data/60POPC_10CHOL_30LBPA16/analys/average_rdf_LBPA.xvg};
\end{axis}
\end{tikzpicture}
\caption{DPPC/CERA/SM16/LBPA}
\end{subfigure}
\caption{{\bf Radial distribution function (RDF) of lipids around cholesterol. RDFs from NPT and FEP simulations averaged. } }
\end{figure}
\clearpage
\subsection{CHOL - contacts (0.6nm)}
\pgfplotsset{contacts/.style={
height=7.5cm,
xlabel={time [ns]},
ylabel={number of atoms},
scaled x ticks={real:1000},
xtick scale label code/.code={},
xmin=0,
xmax=200000,
}}
\begin{figure}[H]
\centering
\tikzsetnextfilename{contacts_r06_POPC}
\begin{tikzpicture}
\begin{axis}[contacts, xmax=500000]
\addplot table {data/90POPC_10CHOL/analys/contacts/numcount_r0.6_POPC_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/contacts/numcount_r0.6_POPC_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/contacts/numcount_r0.6_POPC_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/contacts/numcount_r0.6_POPC_20-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/contacts/numcount_r0.6_POPC_20-mean.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA14/analys/contacts/numcount_r0.6_POPC_20-mean.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA16/analys/contacts/numcount_r0.6_POPC_20-mean.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Number of CHOL-POPC contacts (0.6 nm). } }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{contacts_r06_DPPC}
\begin{tikzpicture}
\begin{axis}[contacts, xmax=500000]
\addplot [DPPC] table {data/60POPC_10CHOL_30DPPC/analys/contacts/numcount_r0.6_DPPC_20-mean.xvg};
\addplot [CERA] table {data/60POPC_10CHOL_30CERA/analys/contacts/numcount_r0.6_CERA_20-mean.xvg};
\addplot [SM16] table {data/60POPC_10CHOL_30SM16/analys/contacts/numcount_r0.6_SM16_20-mean.xvg};
\addplot [LB2R] table {data/60POPC_10CHOL_30LBPA22RR/analys/contacts/numcount_r0.6_LBPA_20-mean.xvg};
%\addplot [LB14] table {data/60POPC_10CHOL_30LBPA14/analys/contacts/numcount_r0.6_LBPA_20-mean.xvg};
%\addplot [LB16] table {data/60POPC_10CHOL_30LBPA16/analys/contacts/numcount_r0.6_LBPA_20-mean.xvg};
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Number of CHOL-DPPC/CERA/SM16/LBPA contacts (0.6 nm). } }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{contacts_r06_Water}
\begin{tikzpicture}
\begin{axis}[contacts, xmax=500000]
\addplot [POPC] table {data/90POPC_10CHOL/analys/contacts/numcount_r0.6_Water_100-mean.xvg};
\addplot [DPPC] table {data/60POPC_10CHOL_30DPPC/analys/contacts/numcount_r0.6_Water_100-mean.xvg};
\addplot [CERA] table {data/60POPC_10CHOL_30CERA/analys/contacts/numcount_r0.6_Water_100-mean.xvg};
\addplot [SM16] table {data/60POPC_10CHOL_30SM16/analys/contacts/numcount_r0.6_Water_100-mean.xvg};
\addplot [LB2R] table {data/60POPC_10CHOL_30LBPA22RR/analys/contacts/numcount_r0.6_Water_100-mean.xvg};
%\addplot [LB14] table {data/60POPC_10CHOL_30LBPA14/analys/contacts/numcount_r0.6_Water_100-mean.xvg};
%\addplot [LB16] table {data/60POPC_10CHOL_30LBPA16/analys/contacts/numcount_r0.6_Water_100-mean.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC }
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Number of CHOL-Water contacts (0.6 nm). } }
\end{figure}
\clearpage
\subsection{Hydrogen bonds}
\pgfplotsset{hbond/.style={
height=7.5cm,
xlabel={time [ns]},
ylabel={number of h-bonds},
scaled x ticks={real:1000},
xtick scale label code/.code={},
xmin=0,
xmax=500000,
}}
\begin{figure}[H]
\centering
\tikzsetnextfilename{hbond_POPC}
\begin{tikzpicture}
\begin{axis}[hbond, xmax=500000]
\addplot table {data/90POPC_10CHOL/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/hbond/CHOL-POPC_100-mean.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Number of CHOL-POPC hydrogen bonds. } }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{hbond_DPPC}
\begin{tikzpicture}
\begin{axis}[hbond, xmax=500000]
\addplot [DPPC] table {data/60POPC_10CHOL_30DPPC/analys/hbond/CHOL-DPPC_100-mean.xvg};
\addplot [CERA] table {data/60POPC_10CHOL_30CERA/analys/hbond/CHOL-CERA_100-mean.xvg};
\addplot [SM16] table {data/60POPC_10CHOL_30SM16/analys/hbond/CHOL-SM16_100-mean.xvg};
\addplot [LB2R] table {data/60POPC_10CHOL_30LBPA22RR/analys/hbond/CHOL-LBPA_100-mean.xvg};
\addplot [LB14] table {data/60POPC_10CHOL_30LBPA14/analys/hbond/CHOL-LBPA_100-mean.xvg};
\addplot [LB16] table {data/60POPC_10CHOL_30LBPA16/analys/hbond/CHOL-LBPA_100-mean.xvg};
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Number of CHOL-DPPC/CERA/SM16/LBPA hydrogen bonds. } }
\end{figure}
\clearpage
\begin{figure}[H]
\centering
\tikzsetnextfilename{hbond_distance_POPC}
\begin{tikzpicture}
\begin{axis}[hbond, xmax=500000,table/y index=2]
\addplot table {data/90POPC_10CHOL/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/hbond/CHOL-POPC_100-mean.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/hbond/CHOL-POPC_100-mean.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Number of CHOL-POPC hydrogen bonds defined by only distance (angle ignored). } }
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{hbond_distance_DPPC}
\begin{tikzpicture}
\begin{axis}[hbond, xmax=500000,table/y index=2]
\addplot [DPPC] table {data/60POPC_10CHOL_30DPPC/analys/hbond/CHOL-DPPC_100-mean.xvg};
\addplot [CERA] table {data/60POPC_10CHOL_30CERA/analys/hbond/CHOL-CERA_100-mean.xvg};
\addplot [SM16] table {data/60POPC_10CHOL_30SM16/analys/hbond/CHOL-SM16_100-mean.xvg};
\addplot [LB2R] table {data/60POPC_10CHOL_30LBPA22RR/analys/hbond/CHOL-LBPA_100-mean.xvg};
\addplot [LB14] table {data/60POPC_10CHOL_30LBPA14/analys/hbond/CHOL-LBPA_100-mean.xvg};
\addplot [LB16] table {data/60POPC_10CHOL_30LBPA16/analys/hbond/CHOL-LBPA_100-mean.xvg};
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{{\bf Number of CHOL-DPPC/CERA/SM16/LBPA hydrogen bonds defined by only distance (angle ignored). } }
\end{figure}
\clearpage
\subsection{POPC Diffusion}
\pgfplotsset{msd/.style={
xmin=0, xmax=500000,
ymin=0,
xlabel={diffusion time [ns]},
scaled x ticks={real:1000},
xtick scale label code/.code={},
ylabel={MSD [nm$^2$]},
each nth point=10,
}}
\pgfplotsset{diffusion/.style={
xmin=0, xmax=500000,
ymin=0, ymax=0.03,
xlabel={diffusion time [ns]},
scaled x ticks={real:1000},
xtick scale label code/.code={},
ylabel={D [nm$^2$/ns]},
table/y expr={\thisrowno{1} / \thisrowno{0} / 4 * 1000},
each nth point=10,
}}
\begin{figure}[H]
\centering
\tikzsetnextfilename{msd_POPC_A}
\begin{tikzpicture}
\begin{axis}[msd]
\addplot table {data/90POPC_10CHOL/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf MSD of POPC in xy-plane. Leaflet A. }}
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{msd_POPC_B}
\begin{tikzpicture}
\begin{axis}[msd]
\addplot table {data/90POPC_10CHOL/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf MSD of POPC in xy-plane. Leaflet B. }}
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{msd_POPC_100ns_A}
\begin{tikzpicture}
\begin{axis}[msd,xmax=100000]
\addplot table {data/90POPC_10CHOL/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf MSD of POPC in xy-plane. 100ns diffusion. Leaflet A. }}
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{msd_POPC_100ns_B}
\begin{tikzpicture}
\begin{axis}[msd,xmax=100000]
\addplot table {data/90POPC_10CHOL/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf MSD of POPC in xy-plane. 100ns diffusion. Leaflet B. }}
\end{figure}
%\begin{figure}[H]
%\centering
%\tikzsetnextfilename{diffusion_POPC}
%\begin{tikzpicture}
%\begin{axis}[diffusion]
%\addplot table {data/90POPC_10CHOL/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addlegendentry{90POPC\_10CHOL}
%\addlegendentry{60POPC\_10CHOL\_30DPPC}
%\addlegendentry{60POPC\_10CHOL\_30CERA}
%\addlegendentry{60POPC\_10CHOL\_30SM16}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
%\end{axis}
%\end{tikzpicture}
%\caption{ {\bf Diffusion coefficient of POPC in xy-plane. Leaflet A. }}
%\end{figure}
%\begin{figure}[H]
%\centering
%\tikzsetnextfilename{diffusion_POPC_B}
%\begin{tikzpicture}
%\begin{axis}[diffusion]
%\addplot table {data/90POPC_10CHOL/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addlegendentry{90POPC\_10CHOL}
%\addlegendentry{60POPC\_10CHOL\_30DPPC}
%\addlegendentry{60POPC\_10CHOL\_30CERA}
%\addlegendentry{60POPC\_10CHOL\_30SM16}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
%\end{axis}
%\end{tikzpicture}
%\caption{ {\bf Diffusion coefficient of POPC in xy-plane. Leaflet B. }}
%\end{figure}
%\begin{figure}[H]
%\centering
%\tikzsetnextfilename{diffusion_POPC_100ns}
%\begin{tikzpicture}
%\begin{axis}[diffusion,xmax=100000]
%\addplot table {data/90POPC_10CHOL/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/POPC/msd_mol_leaflet_A_b50000.xvg};
%\addlegendentry{90POPC\_10CHOL}
%\addlegendentry{60POPC\_10CHOL\_30DPPC}
%\addlegendentry{60POPC\_10CHOL\_30CERA}
%\addlegendentry{60POPC\_10CHOL\_30SM16}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
%\end{axis}
%\end{tikzpicture}
%\caption{ {\bf Diffusion coefficient of POPC in xy-plane. 100ns diffusion. Leaflet A. }}
%\end{figure}
%\begin{figure}[H]
%\centering
%\tikzsetnextfilename{diffusion_POPC_100ns_B}
%\begin{tikzpicture}
%\begin{axis}[diffusion,xmax=100000]
%\addplot table {data/90POPC_10CHOL/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/POPC/msd_mol_leaflet_B_b50000.xvg};
%\addlegendentry{90POPC\_10CHOL}
%\addlegendentry{60POPC\_10CHOL\_30DPPC}
%\addlegendentry{60POPC\_10CHOL\_30CERA}
%\addlegendentry{60POPC\_10CHOL\_30SM16}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
%\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
%\end{axis}
%\end{tikzpicture}
%\caption{ {\bf Diffusion coefficient of POPC in xy-plane. 100ns diffusion. Leaflet B. }}
%\end{figure}
\subsection{CHOL diffusion}
\begin{figure}[H]
\centering
\tikzsetnextfilename{msd_CHOL_A}
\begin{tikzpicture}
\begin{axis}[msd]
\addplot table {data/90POPC_10CHOL/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf MSD of cholesterol in xy-plane. Leaflet A. }}
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{msd_CHOL_B}
\begin{tikzpicture}
\begin{axis}[msd]
\addplot table {data/90POPC_10CHOL/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf MSD of cholesterol in xy-plane. Leaflet B. }}
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{msd_CHOL_100ns_A}
\begin{tikzpicture}
\begin{axis}[msd,xmax=100000]
\addplot table {data/90POPC_10CHOL/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/CHOL/msd_mol_leaflet_A_b50000.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf MSD of cholesterol in xy-plane. 100ns diffusion. Leaflet A. }}
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{msd_CHOL_100ns_B}
\begin{tikzpicture}
\begin{axis}[msd,xmax=100000]
\addplot table {data/90POPC_10CHOL/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/analys/msd/CHOL/msd_mol_leaflet_B_b50000.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf MSD of cholesterol in xy-plane. 100ns diffusion. Leaflet B. }}
\end{figure}
\clearpage
\subsection{Free energy calculations}
\pgfplotsset{fep/.style={
xmin=0, xmax=16, ymin=-14, ymax=1,
width=11cm,
%height=8cm,
minor y tick num={1},
xlabel={$\lambda$},
ylabel={$\Delta$G [kT]},
table/y error plus index = 2,
table/y error minus index = 2,
error bars/y dir=both,
error bars/y explicit,
legend columns=2,
legend style={at={(0,1.05)},anchor=south west},
transpose legend,
}}
\pgfplotsset{fep_small/.style={
xmin=13.5, xmax=15.5, ymax=-8, ymin=-10,
xtick={14,15},
width=6cm,
%height=8cm,
minor y tick num={1},
xlabel={$\lambda$},
ylabel={$\Delta$G [kT]},
table/y error plus index = 2,
table/y error minus index = 2,
error bars/y dir=both,
error bars/y explicit,
}}
\begin{figure}[H]
\begin{subfigure}[b]{0.69\textwidth}
\centering
\tikzsetnextfilename{bar_cumsum_A}
\begin{tikzpicture}
\begin{axis}[fep]
\addplot table {data/90POPC_10CHOL/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\end{subfigure}
\begin{subfigure}[b]{0.29\textwidth}
\centering
\tikzsetnextfilename{bar_cumsum_A_zoom}
\begin{tikzpicture}
\begin{axis}[fep_small]
\addplot table {data/90POPC_10CHOL/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\end{axis}
\end{tikzpicture}
\end{subfigure}
\caption{ {\bf Free energy integral. Leaflet A. } Length of simulations was 100 ns. The different inital structures were created by using different cholesterol molecules and different time frames of NPT-simulation. The plot is simply cumulative sum of $\Delta G$s between lambdas (from bar.xvg file). The error estimate is sum of squares error (SSE) of bootsrap errors.}
\end{figure}
\begin{figure}[H]
\begin{subfigure}[b]{0.69\textwidth}
\centering
\tikzsetnextfilename{bar_cumsum_B}
\begin{tikzpicture}
\begin{axis}[fep]
\addplot table {data/90POPC_10CHOL/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addlegendentry{90POPC\_10CHOL}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\end{subfigure}
\begin{subfigure}[b]{0.29\textwidth}
\centering
\tikzsetnextfilename{bar_cumsum_B_zoom}
\begin{tikzpicture}
\begin{axis}[fep_small]
\addplot table {data/90POPC_10CHOL/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30CERA/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30SM16/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA22RR/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA14/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30LBPA16/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\end{axis}
\end{tikzpicture}
\end{subfigure}
\caption{{\bf Free energy integral. Leaflet B. } Same as figure above, but leaflet B was used for calculation. Simulation length was 100 ns. A flip-flop occurred in LBPA$_{14:0}$ system, and messed up the results.}
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{bar_DPPC}
\begin{tikzpicture}
\begin{axis}[fep_small]
\addplot table {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_A/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_B/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_A_run2/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addplot table {data/60POPC_10CHOL_30DPPC/free_energy/leaflet_B_run2/analys/bar_b100000/1-100000/bar_cumsum_SSE.xvg};
\addlegendentry{60POPC\_10CHOL\_30DPPC\_leafletArep1}
\addlegendentry{60POPC\_10CHOL\_30DPPC\_leafletBrep1}
\addlegendentry{60POPC\_10CHOL\_30DPPC\_leafletArep2}
\addlegendentry{60POPC\_10CHOL\_30DPPC\_leafletBrep2}
\end{axis}
\end{tikzpicture}
\end{figure}
\pgfplotsset{fep_bar/.style={
% BARCHART properties
every axis plot/.append style={fill},
every axis plot/.append style={fill opacity=0.5},
width=16cm,
height=15cm,
ybar=0pt,
xtick={data},
grid=major,
enlarge x limits=0.3,
table/y error plus index=2,
table/y error minus index=2,
error bars/y dir=both,
error bars/y explicit,
legend pos=north west,
bar width=16pt,
}}
\pgfplotstableread{
System DG Error
leafA -8.991000e+00 6.954157e-02
leafB -8.942400e+00 6.818790e-02
avg -8.966900e+00 5.338033e-02
}{\DGTableCERA}
\pgfplotstableread{
System DG Error
leafA -8.423200e+00 7.906535e-02
leafB -8.727400e+00 5.463826e-02
avg -8.576500e+00 1.011496e-01
}{\DGTableDPPC}
\pgfplotstableread{
System DG Error
leafA -9.16200 0.06242
leafB -9.00780 0.07632
avg -9.08480 0.07469
}{\DGTableLBPAfourteen}
\pgfplotstableread{
System DG Error
leafA -8.707200e+00 6.445138e-02
leafB -9.087200e+00 6.802683e-02
avg -8.897000e+00 4.956551e-02
}{\DGTableLBPAsixteen}
\pgfplotstableread{
System DG Error
leafA -9.464600e+00 6.700873e-02
leafB -9.545400e+00 7.246178e-02
avg -9.504700e+00 5.027654e-02
}{\DGTableLBPA}
\pgfplotstableread{
System DG Error
leafA -8.559500e+00 6.429642e-02
leafB -8.422300e+00 6.751726e-02
avg -8.490700e+00 4.429210e-02
}{\DGTableSM}
\pgfplotstableread{
System DG Error
leafA -9.258500e+00 5.809535e-02
leafB -9.107300e+00 7.655155e-02
avg -9.182400e+00 5.040794e-02
}{\DGTablePOPC}
\begin{figure}[H]
\centering
\tikzsetnextfilename{DGbar}
\begin{tikzpicture}
\begin{axis}[fep_bar,
table/y=DG,
symbolic x coords={leafA,leafB,avg},
xticklabels={leaflet A,leaflet B,average},
ylabel={$\Delta$G [kT]},
legend pos=south west,
ymin=-10, ymax=-8.2,
]
\addplot [POPC] table {\DGTablePOPC};
\addplot [DPPC] table {\DGTableDPPC};
\addplot [CERA] table {\DGTableCERA};
\addplot [SM16] table {\DGTableSM};
\addplot [LB2R] table {\DGTableLBPA};
\addplot [LB14] table {\DGTableLBPAfourteen};
\addplot [LB16] table {\DGTableLBPAsixteen};
\addlegendentry{60POPC\_10CHOL\_30POPC}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf$\Delta$G of two leaflets compared. } Error estimate from using bootstrap with {\tt nbmin=6} and {\tt nbmax=10}}
\end{figure}
\begin{figure}[H]
\centering
\tikzsetnextfilename{DDGbar}
\begin{tikzpicture}
\begin{axis}[fep_bar,
table/y=DG,
symbolic x coords={leafA,leafB,avg},
xticklabels={leaflet A,leaflet B,average},
ylabel={$\Delta\Delta$G [kT]},
legend pos=south west,
%ymin=-10, ymax=-8.2,
table/y expr= - \thisrowno{1} - 9.1824,
%table/y error plus expr=\thisrowno{2},
%table/y error minus expr=\thisrowno{2},
table/y error plus expr=\thisrowno{2} + 0.05040794,
table/y error minus expr=\thisrowno{2} + 0.05040794,
]
\addplot [POPC] table {\DGTablePOPC};
\addplot [DPPC] table {\DGTableDPPC};
\addplot [CERA] table {\DGTableCERA};
\addplot [SM16] table {\DGTableSM};
\addplot [LB2R] table {\DGTableLBPA};
\addplot [LB14] table {\DGTableLBPAfourteen};
\addplot [LB16] table {\DGTableLBPAsixteen};
\addlegendentry{60POPC\_10CHOL\_30POPC}
\addlegendentry{60POPC\_10CHOL\_30DPPC}
\addlegendentry{60POPC\_10CHOL\_30CERA}
\addlegendentry{60POPC\_10CHOL\_30SM16}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{18:1}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{14:0}$}
\addlegendentry{60POPC\_10CHOL\_30LBPA$_\text{16:0}$}
\end{axis}
\end{tikzpicture}
\caption{ {\bf Difference of $\Delta$G compared to pure POPC+CHOL system (90POPC\_10CHOL).} }
\end{figure}
\end{document}