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Add data by Antonio Peon from https://github.com/NMRLipids/MATCH/pull…
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…/77/files, except the data with some unclarities: NMRLipids/MATCH#80, NMRLipids/MATCH#79 and NMRLipids/MATCH#78
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ohsOllila committed Aug 27, 2019
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Binary file modified Figs/HGorderparametersPE.eps
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Binary file modified Figs/HGorderparametersPE.pdf
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Binary file modified Figs/HGorderparametersPG.pdf
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12 changes: 8 additions & 4 deletions Figs/scripts/plotOrderParametersPE.gpl
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Expand Up @@ -113,17 +113,19 @@ dxL17pJ = 7*d
# DROSS = Dipolar Recoupling On-axis with Scaling and Shape preservation
# R-PDLF = R-type Proton Detected Local Field

plot [0.5:5.5][0.2:-0.30] \
plot [0.5:5.5][0.25:-0.30] \
horizLines(' ../../../MATCH/Data/Lipid_Bilayers/POPE/T310K/Headgroup_Glycerol_Order_Parameters_Experiments.dat') \
u ($1):(($2)) w l ls 8 lc rgb "#5F5F5F" lw 6.5 t "POPE 310K experiment", \
horizLines(' ../../../MATCH/Data/Lipid_Bilayers/POPE/T310K/Headgroup_Glycerol_Order_Parameters_Experiments.dat') \
u ($1):(($3)) w l ls 8 lc rgb "#5F5F5F" lw 6.5, \
"../../../MATCH/Data/Lipid_Bilayers/POPE/T310K/Slipids/OrdParsPOPEplot.dat" \
u ($1):($2) lt Slipid pt 7 ps r t 'POPE 310K SLIPIDS', \
"../../../MATCH/Data/Lipid_Bilayers/POPE/T310K/MODEL_SLIPID_500lipids/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt Slipid pt 6 ps r t 'POPE 310K SLIPIDS', \
"../../../MATCH/Data/Lipid_Bilayers/POPE/T310K/CHARMM36/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt CHARMM pt 7 ps r t 'POPE 310K CHARMM36',\
"../../../MATCH/Data/Lipid_Bilayers/POPE+150mNaCl/T310K/MODEL_CHARMM36_500lipids/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt CHARMM pt 6 ps r t 'POPE (150 mM Na^+) 310K CHARMM36',\
"../../../MATCH/Data/Lipid_Bilayers/POPE/T310K/MODEL_CHARMM36_500lipids/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt CHARMM pt 6 ps 1.2 t 'POPE 310K CHARMM36',\
"../../../MATCH/Data/Lipid_Bilayers/POPE+150mNaCl/T310K/MODEL_LIPID17_500lipids/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt Lipd17 pt 6 ps r t 'POPE (150 mM Na^+) 310K LIPID17',\
horizLines(' ../../../MATCH/Data/Lipid_Bilayers/DPPE/T341K/Headgroup_Glycerol_Order_Parameters_Experiments.dat') \
Expand All @@ -135,7 +137,9 @@ plot [0.5:5.5][0.2:-0.30] \
horizLines(' ../../../MATCH/Data/Lipid_Bilayers/E.coliPE/T310K/Headgroup_Glycerol_Order_Parameters_Experiments.dat') \
u ($1):($3*0.00784) w l ls 4 lc rgb "#5F5F5F" lw 3 , \
"../../../MATCH/Data/Lipid_Bilayers/DPPE/T336K/MODEL_SLIPIDS/Headgroup_Glycerol_Order_Parameters_Simulations.dat" \
u ($1):($2) lt Slipid pt 12 ps r t 'DPPE 336K SLIPIDS', \
u ($1):($2) lt Slipid pt 12 ps r t 'DPPE 336K SLIPIDS' ,\
"../../../MATCH/Data/Lipid_Bilayers/POPE/T310K/MODEL_GROMOS-CKP/Headgroup_Glycerol_Order_Parameters_Simulations.dat" \
u ($1):($2) lt CKP_QB pt 12 ps r t 'POPE 310K GROMOS-CKP'



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16 changes: 8 additions & 8 deletions Figs/scripts/plotOrderParametersPG.gpl
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Expand Up @@ -124,16 +124,16 @@ plot [0.5:5.5][0.2:-0.30] \
u ($1):($3*0.00784) w l ls 4 lc 16 lw 3 , \
"../../../MATCH/Data/Lipid_Bilayers/POPG/T298K/MODEL_SLIPIDS/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt Slipid pt 6 ps r t 'POPG T298K SLIPIDS', \
"../../../MATCH/Data/Lipid_Bilayers/POPG+150mNaCl/T310K/MODEL_SLIPID_500lipids/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt Slipid pt 7 ps r t 'POPG T310K + 150mM NaCl SLIPIDS', \
"../../../MATCH/Data/Lipid_Bilayers/POPG/T310K/MODEL_SLIPID_500lipids/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt Slipid pt 7 ps r t 'POPG T310K SLIPIDS', \
"../../../MATCH/Data/Lipid_Bilayers/POPG/T298K/MODEL_CHARMM_GUI/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt CHARMM pt 6 ps r t 'POPG T298K CHARMM36',\
"../../../MATCH/Data/Lipid_Bilayers/POPG+150mNaCl/T310K/MODEL_CHARMM36_500lipids/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt CHARMM pt 7 ps r t 'POPG T310K + 150mM NaCl CHARMM36',\
"../../../MATCH/Data/Lipid_Bilayers/POPG+150mNaCl/T310K/MODEL_LIPID17_500lipids/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt Lipd17 pt 7 ps r t 'POPG T310K + 150mM NaCl LIPID17',\
"../../../MATCH/Data/Lipid_Bilayers/POPG+150mNaCl/T310K/MODEL_GROMOS-CKP/OrdParmPOPGforplot.dat" \
u ($1):($2):($4) w ye lt CKP_QK pt 6 ps r t 'POPG T310K+150mM NaCl CKP', \
"../../../MATCH/Data/Lipid_Bilayers/POPG/T310K/MODEL_CHARMM36_500lipids/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt CHARMM pt 7 ps r t 'POPG T310K CHARMM36',\
"../../../MATCH/Data/Lipid_Bilayers/POPG/T310K/MODEL_LIPID17_500lipids/Headgroup_Glycerol_Order_Parameters_Simulation.dat" \
u ($1):($2) lt Lipd17 pt 7 ps r t 'POPG T310K LIPID17',\
"../../../MATCH/Data/Lipid_Bilayers/POPG/T310K/MODEL_GROMOS-CKP/OrdParmPOPGforplot.dat" \
u ($1):($2):($4) w ye lt CKP_QK pt 6 ps r t 'POPG T310K CKP', \
horizLines(' ../../../MATCH/Data/Lipid_Bilayers/DPPG/T314K/Headgroup_Glycerol_Order_Parameters_Experiments.dat') \
u ($1):($2*0.00784) w l ls 4 dt 2 lc rgb "#5F5F5F" lw 3 t "DPPG 314K experiment", \
horizLines(' ../../../MATCH/Data/Lipid_Bilayers/DPPG/T314K/Headgroup_Glycerol_Order_Parameters_Experiments.dat') \
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Binary file modified Manuscript/manuscriptPGPE.pdf
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89 changes: 60 additions & 29 deletions Manuscript/manuscriptPGPE.tex
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Expand Up @@ -172,7 +172,7 @@ \subsection{Molecular dynamics simulations}
\begin{table*}[htb]
%\begin{sidewaystable*}[!p]
\centering
\caption{List of single lipid type MD simulations without additional ions.
\caption{List of MD simulations with PE lipids.
% The salt concentrations calculated as [salt]=N$_{\rm c} \times$[water]\,/\,N$_{\rm w}$, where [water]\,=\,55.5~M.
% these correspond the concentrations reported in the experiments by Akutsu et al.~\cite{akutsu81}.
% The lipid force fields named as in our previous work~\cite{botan15}.
Expand All @@ -181,30 +181,69 @@ \subsection{Molecular dynamics simulations}
\begin{tabular}{l c c r r r r r r c c}
%\hline
% some footnotes are not visible in typeset-MS (pdf)
lipid/counter-ions & force field for lipids / ions & \footnote{Number of lipid molecules with largest mole fraction}N$_{\rm l}$ & \footnote{Number of water molecules}N$_{\rm w}$ & \footnote{Simulation temperature}T (K) & \footnote{Total simulation time}t$_{{\rm sim}}$(ns) & \footnote{Time used for analysis}t$_{{\rm anal}}$ (ns) & \footnote{Reference for simulation files}files\\
lipid/counter-ions & force field for lipids / ions & NaCl (M) & \footnote{Number of lipid molecules with largest mole fraction}N$_{\rm l}$ & \footnote{Number of water molecules}N$_{\rm w}$ & \footnote{Number of additional cations}N$_{\rm c}$ & \footnote{Simulation temperature}T (K) & \footnote{Total simulation time}t$_{{\rm sim}}$(ns) & \footnote{Time used for analysis}t$_{{\rm anal}}$ (ns) & \footnote{Reference for simulation files}files\\
\hline
DPPE & Slipids \cite{jambeck12b} & 288 & 9386 & 336 & 200 & 100 & \cite{slipidsDPPEfiles} \\
DPPE & GROMOS-CKP \cite{??} & 128 & ? & 342 & 2$\times$500 & 2$\times$400 & \cite{gromosCKPdppe} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
POPE & CHARMM36 \cite{??} &0 & 144 & 5760 &0 & 310 & 500 & 400 & \cite{charmm36POPEfiles} \\
POPE & CHARMM36 \cite{??} & 0 & 500 & 25000 & 0 & 310 & 500 & 100 & \cite{POPEcharmm} \\
POPE & CHARMM36 \cite{??} & 0.11 & 500 & 25000 & 50 & 310 & 500 & 100 & \cite{POPEcharmm150mMNaCl} \\
POPE & CHARMM36ua \cite{??} &0 & 336 & ? &0 & 310 & 2$\times$200 & 2$\times$100 & \cite{charmm36uaPOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
\hline
POPE & GROMOS 43A1-S3 \cite{??} & 128 & ? & 313 & 2$\times$200 & 2$\times$100 & \cite{gromos43a1s3POPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
POPE & CHARMM36ua \cite{??} & 336 & ? & 310 & 2$\times$200 & 2$\times$100 & \cite{charmm36uaPOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
POPE & CHARMM36 \cite{??} & 144 & 5760 & 310 & 500 & 400 & \cite{charmm36POPEfiles} \\
POPE & Slipids \cite{jambeck12b,??} & 336 & ? & 310 & 2$\times$200 & 2$\times$100 & \cite{slipidsPOPEfiles} \\
POPE & OPLS-UA vdW on H \cite{??} & 128 & ? & 303 & 2$\times$200 & 2$\times$100 & \cite{OPLSuaWvdWPOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
POPE & OPLS-UA \cite{??} & 128 & ? & 303 & 2$\times$200 & 2$\times$100 & \cite{OPLSuaPOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
POPE & Berger-based \cite{??} & 128 & ? & 303 & 2$\times$200 & 2$\times$100 & \cite{bergerPOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
POPE & Berger-based2 \cite{??} & 128 & ? & 303 & 2$\times$200 & 2$\times$100 & \cite{berger2POPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
POPE & GROMOS-CKP \cite{??} & 128 & ? & 313 & 2$\times$500 & 2$\times$400 & \cite{gromosCKPpope} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
DPPE & Slipids \cite{jambeck12b} &0 & 288 & 9386 &0 & 336 & 200 & 100 & \cite{slipidsDPPEfiles} \\
POPE & Slipids \cite{jambeck12b,??} &0 & 336 & ? &0 & 310 & 2$\times$200 & 2$\times$100 & \cite{slipidsPOPEfiles} \\
POPE & Slipids \cite{??} \todoi{Ion parameters?} & 0 & 500 & 25000 & 0 & 310 & 500 & 100 & \cite{POPEslipids} \\
POPE & Slipids \cite{??} \todoi{Ion parameters?} & 0.11 & 500 & 25000 & 50 & 310 & 500 & 100 & \cite{POPEslipids150mMNaCl} \\
\hline
DOPE & Berger-based \cite{??} & 128 & ? & 271 & 2$\times$200 & 2$\times$100 & \cite{bergerDOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
DOPE & Berger-based2 \cite{??} & 128 & ? & 271 & 2$\times$300 & 2$\times$100 & \cite{berger2DOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
DOPE & GROMOS-CKP \cite{??} & 128 & ? & 271 & 2$\times$500 & 2$\times$400 & \cite{gromosCKPdope} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
DPPE & GROMOS-CKP \cite{??} &0 & 128 & ? &0 & 342 & 2$\times$500 & 2$\times$400 & \cite{gromosCKPdppe} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
POPE & GROMOS-CKP \cite{??} &0 & 128 & ? &0 & 313 & 2$\times$500 & 2$\times$400 & \cite{gromosCKPpope} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
POPE & GROMOS-CKP \cite{??} &0 & 500 & 25000 &0 & 310 & 500 & 100 & \cite{gromosCKPpopeT310} \\
DOPE & GROMOS-CKP \cite{??} &0 & 128 & ? &0 & 271 & 2$\times$500 & 2$\times$400 & \cite{gromosCKPdope} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
\hline
POPG/K$^+$ & CHARMM36 \cite{??} \todoi{Correct citation for CHARMM POPG} & 118& 4110 & 298 & 100 & 100 & \cite{CHARMM36popg} \\
POPG/Na$^+$ & Slipids \cite{jambeck13} & 288 & 10664 & 298 & 250 & 100 & \cite{slipidsPOPGfiles} \\
POPE & GROMOS 43A1-S3 \cite{??} &0 & 128 & ? &0 & 313 & 2$\times$200 & 2$\times$100 & \cite{gromos43a1s3POPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
\hline
DPPG/Na$^+$ & Slipids \cite{jambeck13} & 288 & 11232 & 314 & 200 & 100 & \cite{slipidsDPPGfiles} \\
DPPG/Na$^+$ & Slipids \cite{jambeck13} & 288 & 11232 & 298 & 400 & 100 & \cite{slipidsDPPGfilesT298K} \\
POPE & OPLS-UA vdW on H \cite{??} &0 & 128 & ? &0 & 303 & 2$\times$200 & 2$\times$100 & \cite{OPLSuaWvdWPOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
POPE & OPLS-UA \cite{??} &0 & 128 & ? &0 & 303 & 2$\times$200 & 2$\times$100 & \cite{OPLSuaPOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
\hline
POPE & Berger-based \cite{??} &0 & 128 & ? &0 & 303 & 2$\times$200 & 2$\times$100 & \cite{bergerPOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
POPE & Berger-based2 \cite{??} &0 & 128 & ? &0 & 303 & 2$\times$200 & 2$\times$100 & \cite{berger2POPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
DOPE & Berger-based \cite{??} &0 & 128 & ? &0 & 271 & 2$\times$200 & 2$\times$100 & \cite{bergerDOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
DOPE & Berger-based2 \cite{??} &0 & 128 & ? &0 & 271 & 2$\times$300 & 2$\times$100 & \cite{berger2DOPEfiles} \todoi{Not analyzed yet, waiting for the code for UA simulations.} \\
\hline
% POPE & LIPID17 \cite{??} & 0 & 500 & 25000 & 50 & 310 & 500 & 100 & \cite{POPElipid17150mMNaCl} \\
POPE & LIPID17 \cite{??} & 0.11 & 500 & 25000 & 50 & 310 & 500 & 100 & \cite{POPElipid17150mMNaCl} \\
\end{tabular}
\end{minipage}
%\end{sidewaystable*}
\end{table*}

\begin{table*}[htb]
%\begin{sidewaystable*}[!p]
\centering
\caption{List of MD simulations with PG lipids.
% The salt concentrations calculated as [salt]=N$_{\rm c} \times$[water]\,/\,N$_{\rm w}$, where [water]\,=\,55.5~M.
% these correspond the concentrations reported in the experiments by Akutsu et al.~\cite{akutsu81}.
% The lipid force fields named as in our previous work~\cite{botan15}.
}\label{systemsII}
\begin{minipage}[t]{\textwidth}
\begin{tabular}{l c c r r r r r r c c}
%\hline
% some footnotes are not visible in typeset-MS (pdf)
lipid/counter-ions & force field for lipids / ions & NaCl (M) & \footnote{Number of lipid molecules with largest mole fraction}N$_{\rm l}$ & \footnote{Number of water molecules}N$_{\rm w}$ & \footnote{Number of additional cations}N$_{\rm c}$ & \footnote{Simulation temperature}T (K) & \footnote{Total simulation time}t$_{{\rm sim}}$(ns) & \footnote{Time used for analysis}t$_{{\rm anal}}$ (ns) & \footnote{Reference for simulation files}files\\
\hline
POPG/K$^+$ & CHARMM36 \cite{??} \todoi{Correct citation for CHARMM POPG} &0 & 118& 4110 &0 & 298 & 100 & 100 & \cite{CHARMM36popg} \\
POPG & CHARMM36 \cite{??} & 0.11 & 500 & 25000 & 49 & 310 & 500 & 100 & \cite{POPGcharmm150mMNaCl} \\
POPG & CHARMM36 \cite{??} & 0 & 500 & 25000 & 0 & 310 & 500 & 100 & \cite{POPGcharmm} \\
\hline
POPG/Na$^+$ & Slipids \cite{jambeck13} &0 & 288 & 10664 &0 & 298 & 250 & 100 & \cite{slipidsPOPGfiles} \\
DPPG/Na$^+$ & Slipids \cite{jambeck13} &0 & 288 & 11232 &0 & 314 & 200 & 100 & \cite{slipidsDPPGfiles} \\
DPPG/Na$^+$ & Slipids \cite{jambeck13} &0 & 288 & 11232 &0 & 298 & 400 & 100 & \cite{slipidsDPPGfilesT298K} \\
POPG & Slipids \cite{??} \todoi{Ion parameters?} & 0 & 500 & 25000 & 0 & 310 & 500 & 100 & \cite{POPGslipids} \\
POPG & Slipids \cite{??} \todoi{Ion parameters?} & 0.11 & 500 & 25000 & 49 & 310 & 500 & 100 & \cite{POPGslipids150mMNaCl} \\
\hline
POPG & LIPID17 \cite{??} & 0 & 500 & 25000 & 0 & 310 & 500 & 100 & \cite{POPGlipid17} \\
POPG & LIPID17 \cite{??} & 0.11 & 500 & 25000 & 49 & 310 & 500 & 100 & \cite{POPGlipid17150mMNaCl} \\
\hline
POPG & GROMOS-CKP \cite{??} & 0 & 500 & 25000 & 0 & 310 & 500 & 100 & \cite{POPGgromosCKP} \\
POPG & GROMOS-CKP \cite{??} & 0.11 & 500 & 25000 & 0 & 310 & 500 & 100 & \cite{POPGgromosCKP150mMNaCl} \\
\end{tabular}
\end{minipage}
%\end{sidewaystable*}
Expand All @@ -213,7 +252,7 @@ \subsection{Molecular dynamics simulations}
\begin{table*}[htb]
%\begin{sidewaystable*}[!p]
\centering
\caption{List of MD simulations with lipid mixtures and additional ions.
\caption{List of MD simulations with PE and PG lipids mixed with PC.
% The salt concentrations calculated as [salt]=N$_{\rm c} \times$[water]\,/\,N$_{\rm w}$, where [water]\,=\,55.5~M.
% these correspond the concentrations reported in the experiments by Akutsu et al.~\cite{akutsu81}.
% The lipid force fields named as in our previous work~\cite{botan15}.
Expand Down Expand Up @@ -245,14 +284,6 @@ \subsection{Molecular dynamics simulations}
\hline
DOPC & Berger \cite{??} \todoi{This is probable not plain berger, correct force filed should be described.} &0 & 0 & 256 & 11008 & 0 & 300 & 300 & 200 & \cite{DOPCberger300K} \\
DOPC:DOPE (1:1) & Berger \cite{??} \todoi{This is probable not plain berger, correct force filed should be described.} &0 & 0 & 128 & 11008 & 0 & 300 & 300 & 200 & \cite{DOPC1DOPE1berger} \\
\hline
POPG & Slipids \cite{??} \todoi{Ion parameters?} & 0.11 & 0 & 500 & 25000 & 49 & 310 & 500 & 100 & \cite{POPGslipids150mMNaCl} \\
POPG & CHARMM36 \cite{??} & 0.11 & 0 & 500 & 25000 & 49 & 310 & 500 & 100 & \cite{POPGcharmm150mMNaCl} \\
POPG & LIPID17 \cite{??} & 0.11 & 0 & 500 & 25000 & 49 & 310 & 500 & 100 & \cite{POPGlipid17150mMNaCl} \\
\hline
POPE & Slipids \cite{??} \todoi{Ion parameters?} & 0.11 & 0 & 500 & 25000 & 50 & 310 & 500 & 100 & \cite{POPEslipids150mMNaCl} \\
POPE & CHARMM36 \cite{??} & 0.11 & 0 & 500 & 25000 & 50 & 310 & 500 & 100 & \cite{POPEcharmm150mMNaCl} \\
POPE & LIPID17 \cite{??} & 0.11 & 0 & 500 & 25000 & 50 & 310 & 500 & 100 & \cite{POPElipid17150mMNaCl} \\
\end{tabular}
\end{minipage}
%\end{sidewaystable*}
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