\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}; \addplot+[name path=minuserror,draw=none,no markers,forget plot] table [comment chars={@,\#}, x index=0,y expr=\thisrowno{1}-\thisrowno{2}] {#2}; \addplot+[forget plot,fill={},opacity=0.5,#1] fill between[on layer={},of=pluserror and minuserror]; \addplot+[no markers,#1] table[comment chars={@,\#}, x index=0, y index=1] {#2}; } \pgfplotsset{ select row/.style={ x filter/.code={\ifnum\coordindex=#1\else\def\pgfmathresult{}\fi} } } % 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}