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diff --git a/Data/POPS/OP_exp_oleoyl.dat b/Data/POPS/OP_exp_oleoyl.dat
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diff --git a/Data/POPS/OP_exp_palmitoyl.dat b/Data/POPS/OP_exp_palmitoyl.dat
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diff --git a/Data/POPS/crowded_region.pdf b/Data/POPS/crowded_region.pdf
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+/Helvetica /WindowsLatin1Encoding 120 FMSR
+
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+(0.5) s
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+(1) s
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+gr
+
+24 w
+%%IncludeResource: font Helvetica
+/Helvetica /WindowsLatin1Encoding 96 FMSR
+
+2599 7579 mt 
+(1) s
+%%IncludeResource: font Helvetica
+/Helvetica /WindowsLatin1Encoding 120 FMSR
+
+2652 7639 mt 
+(H-) s
+%%IncludeResource: font Helvetica
+/Helvetica /WindowsLatin1Encoding 96 FMSR
+
+2808 7579 mt 
+(13) s
+%%IncludeResource: font Helvetica
+/Helvetica /WindowsLatin1Encoding 120 FMSR
+
+2914 7639 mt 
+(C dipolar field / kHz) s
+gs 2881 6592 783 718 rc
+12 w
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+0 -20 -36 20 36 20 0 -20 3398 6645 5 MP
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+0 0 0 20 36 -20 -36 -20 0 20 3145 6645 6 MP stroke
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+
+6 w
+1 sg
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+0 sg
+%%IncludeResource: font Helvetica
+/Helvetica /WindowsLatin1Encoding 96 FMSR
+
+2881 6536 mt 
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+1 sg
+-234 0 0 -158 234 0 3453 6581 4 MP
+PP
+0 sg
+3477 6536 mt 
+(0.12) s
+
+end %%Color Dict
+
+eplot
+%%EndObject
+
+epage
+end
+
+showpage
+
+%%Trailer
+%%EOF
diff --git a/Manuscript/manuscript.pdf b/Manuscript/manuscript.pdf
new file mode 100644
index 0000000..b9aea09
Binary files /dev/null and b/Manuscript/manuscript.pdf differ
diff --git a/Manuscript/manuscript.tex b/Manuscript/manuscript.tex
index 060afad..fbdcc68 100644
--- a/Manuscript/manuscript.tex
+++ b/Manuscript/manuscript.tex
@@ -3,7 +3,7 @@
 %% The document class accepts keyval options, which should include 
 %% the target journal and optionally the manuscript type. 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-\documentclass[journal=jpcbfk,manuscript=article]{achemso} 
+\documentclass[journal=jctcce,manuscript=article]{achemso} 
  
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %% Place any additional packages needed here.  Only include packages 
@@ -78,7 +78,7 @@
 \newlength{\figwidthsmall}
 \setlength{\figwidthsmall}{6 cm} 
 \newlength{\figwidthfull}
-\setlength{\figwidthfull}{14 cm} 
+\setlength{\figwidthfull}{16 cm} 
 \newlength{\figheightsmall}
 \setlength{\figheightsmall}{6 cm} 
 \newlength{\figheight}
@@ -108,52 +108,28 @@
  
 \author{Josef Melcr} 
 \email{melcr@marge.uochb.cas.cz} 
-%%\homepage[]{https://jmelcr.github.io/}
-\affiliation{Institute of Organic Chemistry and Biochemistry, 
-Academy of Sciences of the Czech Republic,  
-Prague 6, Czech Republic} 
-\author{Tiago Ferreira}
+\affiliation[Czech Academy of Sciences]{Institute of Organic Chemistry and Biochemistry of the 
+Czech Academy of Sciences, Flemingovo n\'{a}m. 542/2, CZ-16610 Prague 6, Czech Republic}
+\alsoaffiliation{Groningen Biomolecular Sciences and Biotechnology Institute 
+and The Zernike Institute for Advanced Materials, 
+University of Groningen, 9747 AG Groningen, The Netherlands}
+
+\author{Tiago M. Ferreira}
 \affiliation{NMR group - Institut for Physics, Martin-Luther University Halle-Wittenberg} 
 \author{Pavel Jungwirth} 
 %%\homepage[]{http://jungwirth.uochb.cas.cz/}
 \affiliation{Institute of Organic Chemistry and Biochemistry, 
-Academy of Sciences of the Czech Republic,  
+Czech Academy of Sciences,  
 Prague 6, Czech Republic} 
-\alsoaffiliation{Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 
-Tampere, Finland} 
 \author{O. H. Samuli Ollila} 
 \email{samuli.ollila@helsinki.fi} 
 %%\homepage[]{Your web page} 
 \affiliation{Institute of Organic Chemistry and Biochemistry, 
-Academy of Sciences of the Czech Republic,  
+Czech Academy of Sciences,  
 Prague 6, Czech Republic} 
 \alsoaffiliation{Institute of Biotechnology, University of Helsinki} 
  
  
-%\author{Andrew N. Other} 
-%\altaffiliation{A shared footnote} 
-%\author{Fred T. Secondauthor} 
-%\altaffiliation{Current address: Some other place, Othert\"own, 
-%Germany} 
-%\author{I. Ken Groupleader} 
-%\altaffiliation{A shared footnote} 
-%\email{i.k.groupleader@unknown.uu} 
-%\phone{+123 (0)123 4445556} 
-%\fax{+123 (0)123 4445557} 
-%\affiliation[Unknown University] 
-%{Department of Chemistry, Unknown University, Unknown Town} 
-%\alsoaffiliation[Second University] 
-%{Department of Chemistry, Second University, Nearby Town} 
-%\author{Susanne K. Laborator} 
-%\email{s.k.laborator@bigpharma.co} 
-%\affiliation[BigPharma] 
-%{Lead Discovery, BigPharma, Big Town, USA} 
-%\author{Kay T. Finally} 
-%\affiliation[Unknown University] 
-%{Department of Chemistry, Unknown University, Unknown Town} 
-%\alsoaffiliation[Second University] 
-%{Department of Chemistry, Second University, Nearby Town} 
- 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %% The document title should be given as usual. Some journals require 
 %% a running title from the author: this should be supplied as an 
@@ -165,16 +141,9 @@
 %   via combination of experiments and molecular simulation}
 
 \title[] 
-{Improved Cation Binding to Lipid Bilayer with Negatively Charged POPS by Effective Inclusion of Electronic Polarization}
-  %Detailed structure of negatively charged membranes 
-  %  of phosphatidylserine and phosphatidylcholine 
-  %  at concentrations of calcium, sodium and potassium salts
-  %  from molecular dynamics simulations with electronic polarization }
-  % JOSEF: I feel that the above title is a bit better, because it focuses on PS,
-  %        but the following one is an alternative, which focuses more on the cations as in roux90
-  %{ Detailed structure of calcium, sodium and potassium cations
-  %  at negatively charged membranes of phosphatidylserine and phosphatidylcholine 
-  %  from molecular dynamics simulations with electronic polarization }
+      {Improved Cation Binding to Lipid Bilayer with
+Negatively Charged POPS by Effective
+Inclusion of Electronic Polarization}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %% Some journals require a list of abbreviations or keywords to be 
@@ -200,21 +169,8 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 \begin{tocentry} 
  
-Some journals require a graphical entry for the Table of Contents. 
-This should be laid out ``print ready'' so that the sizing of the 
-text is correct. 
- 
-Inside the \texttt{tocentry} environment, the font used is Helvetica 
-8\,pt, as required by \emph{Journal of the American Chemical 
-Society}. 
- 
-The surrounding frame is 9\,cm by 3.5\,cm, which is the maximum 
-permitted for  \emph{Journal of the American Chemical Society} 
-graphical table of content entries. The box will not resize if the 
-content is too big: instead it will overflow the edge of the box. 
- 
-This box and the associated title will always be printed on a 
-separate page at the end of the document. 
+\includegraphics[height=1.375 in]{../img/TOC_graphic.pdf} 
+
  
 \end{tocentry} 
  
@@ -227,19 +183,20 @@
  
 \begin{abstract} 
   Phosphatidylserine (PS) lipids are important signaling molecules and the most common negatively charged lipids in eukaryotic membranes.
-  The signaling can be often regulated with calcium, but its interactions with PS headgroups are not fully understood.
+  The signaling can be often regulated by calcium, but its interactions with PS headgroups are not fully understood.
   Classical molecular dynamics (MD) simulations can potentially give detailed description of lipid-ion interactions,
-  but the results strongly depend on the used force field.
-  Here, we apply the electronic continuum correction (ECC) to the Amber Lipid17 parameters of POPS lipid to improve its
-  interactions with Na$^+$ and Ca$^{2+}$ ions.
+  but the results strongly depend on the used force field. Here, we apply the electronic continuum correction (ECC) to
+  the Amber Lipid17 parameters of 1-palmitoyl-2-oleoyl-{\it sn}-glycero-3-phospho-L-serine (POPS) lipid to improve its
+  interactions with \ce{K^+}, Na$^+$ and Ca$^{2+}$ ions.
   The partial charges of headgroup, glycerol backbone and carbonyls of POPS, bearing a unit negative charge, were scaled with a
   factor of 0.75, derived for monovalent ions and the Lennard-Jones $\sigma$ parameters of the same segments were scaled with a factor of 0.89.
-  The resulting ECC-POPS models, gives more realistic interactions with Na$^+$ and Ca$^{2+}$ cations than the original Amber Lipid17 parameters,
-  when validated using the headgroup order parameters and ''electrometer concept''.
-  In ECC-lipids simulations, the Ca$^{2+}$ cations do not simultaneously interact with more than two PS lipids, and interactions 
-  carboxylate groups is twice more likely than with phosphate group, while interaction with carbonyls is almost negligible.
-  Our results pave the way for more realistic MD simulations of anionic biological membranes and demonstrate the ECC
-  approach is useful also for charged lipids.
+  The resulting ECC-POPS model gives more realistic interactions with Na$^+$ and Ca$^{2+}$ cations than the original Amber Lipid17 parameters,
+  when validated using headgroup order parameters and the ''electrometer concept''.
+  In ECC-lipids simulations, populations of complexes of Ca$^{2+}$ cations with more than two PS lipids are negligible, 
+and interactions of Ca$^{2+}$ cations with only carboxylate groups is twice more likely than with only phosphate groups, 
+while interactions with carbonyls almost entirely involve also other groups. 
+  Our results pave the way for more realistic MD simulations of biomolecular systems with anionic membranes
+allowing to elucidate signaling processes involving PS and \ce{Ca^{2+}}. 
 \end{abstract} 
  
  
@@ -269,17 +226,19 @@ \section{Introduction}
 and important signaling molecules \cite{lemmon08,leventis10,li14}.
 They interact with signaling proteins \cite{leventis10},
 regulate surface charge and protein localization \cite{yeung08}, 
-induce protein aggregation \cite{zhao04,gorbenko06} and membrane fusion \cite{??}.
-Because these functions are also often regulated by biological cations \cite{leventis10},
-the detailed interactions between PS lipids and biological cations, like calcium, are under great interest.
-\todo{Pavel can probably improve and complement this}
-
-Spectroscopic experiments give detailed information about the
+induce protein aggregation \cite{zhao04,gorbenko06} and membrane fusion \cite{wilschut1981calcium, papahadjopoulos90, verma2018cell}.
+As such lipid-related functions are also often regulated by ions \cite{leventis10},
+a detailed understanding of interactions between negatively charged lipids and biologically relevant cations such as calcium is of a great importance.
+Recent combination of spectroscopic experiments, biochemical essays, and molecular simulations showed that binding of
+calcium to \ce{PIP_2} lipids inhibits their recognition by a phospolipase~C, 
+which demonstrates that not only proteins but also lipids can get involved in calcium signaling \cite{Bilkova2017Calcium}.
+
+Spectroscopic experiments give accurate information about the
 interactions between ions and PS lipids, but the data is often indirect and difficult to
 interpret \cite{hauser77,kurland79,eisenberg79,hauser83,dluhy83,hauser85,feigenson86,mattai89,roux90,roux91}.
 Some studies suggest that the
-binding constant of ions to negatively charged lipids is similar to that of zwitterionic lipids,
-and the binding affinity is increased only due to the increased cation
+binding affinity of ions to negatively charged lipids is similar to that of zwitterionic lipids,
+and that the amount of bound ions increases only due to the increased cation
 concentration in the vicinity of the membrane \cite{seelig90,sinn06}.
 On the other hand, calcium forms dehydrated complexes with PS headgroups
 which cause phase separation \cite{hauser77,kurland79,hauser85,feigenson86,mattai89,roux90,roux91,boettcher11}.
@@ -298,13 +257,13 @@ \section{Introduction}
 On the other hand, simulations with the Berger force field \cite{berger97,mukhopadhyay04}
 suggest a significant calcium binding also to the carbonyls in the acyl chains \cite{melcrova16}.
 
-The NMRlipids project \url{nmrlipids.blogspot.fi} has recently demonstrated
+The NMRlipids project (\url{nmrlipids.blogspot.fi}) has recently demonstrated
 that such controversies can be resolved by using the headgroup order parameters
 of phosphatidylcholine (PC) lipids \cite{catte16, NMRlipidsIV}, which can
 be related to cation binding affinity to lipid bilayers using the electrometer
-concept \cite{akutsu81,altenbach84,seelig87}. The main advantage of the approach
+concept \cite{akutsu81,altenbach84,seelig87}. The main advantage of this approach
 is the direct comparison between experimental and calculated order parameters,
-which reduced the ambiguity arising from the interpretation of the data.
+which reduce the ambiguity arising from the interpretation of the data.
 Unfortunately, none of the readily available force fields was sufficiently accurate to correctly reproduce the
 cation binding affinity to zwitterionic PC bilayers \cite{catte16} or to the
 mixtures with negatively charged PS lipids \cite{NMRlipidsIV}.
@@ -312,17 +271,9 @@ \section{Introduction}
 to zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer
 by implicitly including electronic polarizability using the electronic continuum
 correction (ECC) \cite{leontyev09}. The good agreement between the resulting ECC-POPC
-model and experiments enable detailed interpretation of calcium binding details to POPC lipid bilayer.
+model and experiments enables a more detailed molecular interpretation of the calcium binding to a POPC lipid bilayer.
 
-%There are force field parameters for neutral lipids PC and PE 
-%with explicit polarizability using the Classical Durde model. \cite{chowdhary13, chowdhary17}
-%While such a model shows a potential improvement over non-polarizable force fields from many perspectives -- 
-%for example accounting for polarizability has a significant impact on the dipole potential of a membrane \cite{harder2009} -- 
-%the non-polarizable version of the same force field 
-%performes comparably well at a fraction of the computational cost 
-%of the models with explicit polarization. \citep{lucas12,chowdhary13} 
-
-Here, we extend the ECC approach also to the negatively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS) lipid.
+Here, we extend the ECC approach also to the negatively charged 1-palmitoyl-2-oleoyl-{\it sn}-glycero-3-phospho-L-serine (POPS) lipid.
 We also complement the available experimental data for the force field quality
 evaluation by measuring the acyl chain C--H bond order parameters of POPS in bilayer using natural abundance $^{13}$C NMR.
 In addition to the acyl chain order parameters measured here, the quality of the newly developed ECC-POPS force field parameters is
@@ -337,26 +288,25 @@ \section{Methods}
  
 \subsection{Electronic continuum correction for PS lipids}\label{section:ecc} 
 
-Electronic continuum correction (ECC) is an implicit mean-field representation of 
-the electronic polarization in classical MD simulations. 
-For simple ions in water, the electronic polarizability
-can be taken into account by scaling the charge with a constant factor 
-%\begin{equation}
- \mbox{$ f_q = \frac{1}{\sqrt{\epsilon_{el}}} \approx 0.75$,}
-%\end{equation}
-where  $\epsilon_{el} = 1.78$ is the high-frequency dielectric constant of electrons in water \cite{leontyev09}.
-The scaling of charges with this factor has been recently applied to improve classical models for ions and
-other biomolecules \cite{Pluharova2014, martinek17, duboue2018insulin, Mason2019, Duboue2018MgZn} \todo{Pavel can probably update this (insulin?)}.
-In addition to the charge, the Lennard-Jones~$\sigma$ was scaled with a factor $f_\sigma \leq 1$
-to improve the hydration properties of ions with respect to scattering data in these studies
-\todo{Pavel can probably deliver the state of the art information about these parameters and sharpen the discussion}.
-
-Derivation of the correct scaling factor for lipids is more complicated, because
-the partial charges depend on the methods used to derive the respective force fields.
-For example, the partial charges may already include the effects of electronic polarizability to some extent,
-and hence, the scaling factor can be larger than the theoretically derived value for ions in water, $f_q \approx 0.75$.
+Electrostatic interactions between charges in a dielectric medium are attenuated by a factor equal to the
+corresponding relative permittivity (dielectric constant). Standard non-polarizable force fields are capable to
+account for the dielectric response from the orientation of the solvent molecules (low-frequency nuclear response), but fail to account for the electronic (high frequency) polarization.
+In most biologically relevant environments this high frequency dielectric constant is approximately 2 (for water the value is 1.78).
+This means that for a non-polarizable force field that would strictly account only for the low-frequency dielectric response
+interactions between charges in aqueous environments should be further attenuated by a factor of 1.78, which is mathematically
+equivalent by scaling the charges by a factor of ~0.75 \cite{leontyev09,leontyev14}. 
+This electronic continuum correction (ECC), which can be view as a mean-field continuum way for accounting for electronic polarization,
+has been shown to significantly improve the description of interactions between aqueous ions and biologically relevant charged groups \cite{pluharova13,kohagen14,kohagen14b,melcr18,xie16,kroutil17,bruce18}
+This correction is particularly important for high charge density species where it helps to remove artifacts such as excessive ion pairing in water~\cite{pluharova13,vazdar13}.
+One should, however, bear in mind that existing non-polarizable force fields have been parameterized also using experimental data, which means that they may to a certain extent include implicitly electronic polarization effects. Therefore, in such cases a charge scaling factor between 0.75 and 1 should carefully be adjusted such that the electronic polarization effects are not overaccounted.    
+In addition to the charge, the Lennard-Jones parameter~$\sigma$ of the ions needed to be modified 
+to improve the description of hydration properties of ions with respect to scattering data in these studies 
+by scaling with a factor $ 0.72 < f_\sigma \leq 1$.
+The reason for the small readjustment of the ionic radii is that the original force fields were often developed such that the first peak on the experimental ion-water oxygen radial distribution function was reproduced. 
+Upon charge scaling this peak typically moved to slightly larger distances and the agreement with experiment was then restored by a small decrease of the Lennard-Jones~$\sigma$ parameter.
+
 Before the ECC theory was rigorously derived, similar idea was already employed in early classical 
-MD simulations of lipids and surfactants using the scaling factor of 0.5 for atomic charges  \cite{jonsson86,egberts94, berendsen1996}. 
+MD simulations of lipids and surfactants using the ad hoc scaling factor of 0.5 for atomic charges  \cite{jonsson86,egberts94, berendsen1996}. 
 In our recent work, we applied the ECC to the Amber based lipid14 force field of zwitterionic POPC lipid \cite{dickson14}
 by scaling the partial charges and Lennard-Jones~$\sigma$ parameters of headgroup, glycerol backbone,
 and carbonyl regions \cite{melcr18}. The scaling factors were optimized to reproduce 
@@ -364,20 +314,17 @@ \subsection{Electronic continuum correction for PS lipids}\label{section:ecc}
 and the electrometer concept \cite{akutsu81,altenbach84,seelig87,catte16}, and the X-ray scattering form factor
 without additional ions \cite{kucerka11}, which resulted to the scaling factor values of $f_q = 0.8$ and $f_\sigma = 0.89$  \cite{melcr18}.
 
-Here, we apply the ECC to the Amber-based lipid17 parameters \cite{lipid17-future} of POPS lipid with a monovalent negative charge.
-Because POPS carries a physical total charge as aqueous ions, we apply the theoretically derived scaling factor for
-ions $f_q = 0.75$ \cite{leontyev09} to the partial charges of POPS. 
-The lipids with a total charge of -0.75 are also neutralized
+Here, we apply the ECC to the Amber Lipid17 parameters of POPS \cite{lipid17-future} (available in AmberTools18 \cite{amber18}). 
+Because POPS is anionic at physiological pH $\approx 7$ carrying a physical total charge as aqueous ions, 
+we apply the scaling factor derived for
+ions\cite{leontyev09} $f_q = 0.75$ to the partial charges of POPS 
+in the headgroup, glycerol backbone, and carbonyl regions. The POPS lipids with a total charge of -0.75 are also neutralized
 by the counterion charges of +0.75 in simulations with ECC-ions \cite{Pluharova2014, kohagen16, martinek17}.
-Following our previous work for POPC, we use the scaling factor of $f_\sigma = 0.89$ for the Lennard-Jones~$\sigma$ parameters and
-use it to scale the parameters of atoms only in the headgroup, glycerol backbone, and carbonyl regions \cite{melcr18}.
+Following our previous work for POPC, we use the scaling factor $f_\sigma = 0.89$ for the Lennard-Jones~$\sigma$ parameters 
+to scale the corresponding parameters of atoms 
+in the headgroup, glycerol backbone, and carbonyl regions \cite{melcr18}. 
 Further optimization of parameters was not done in this work. 
-The generated ECC-POPS parameters are available from Ref.~\citenum{??}
-\todo{We need here a permanent citation with DOI.
-  Easiest would be to add the parameters into a one of the existing Zenodo repositories containing other simulation parameters.
-  We could also put a release of Git into Zenodo, cite that and specify the exact directory where parameters are found,
-  but this is more complicated for users to find.
-}
+The generated ECC-POPS parameters are openly available for download from Ref.~\citenum{ecclipids_pcps_nacl_kcl_series}. 
 
 
 \subsection{Measurements of acyl chain order parameters}
@@ -388,7 +335,7 @@ \subsection{Measurements of acyl chain order parameters}
 \end{equation}
   where $\theta$ denotes the angle of the C--H bond
 with the bilayer normal and the angular brackets define a time average on a time scale of approximately 1 microsecond.
-The experiment was done using a Bruker Avance III 400 spectrometer operating at a 1H Larmor frequency of 400.03 MHz
+The experiment was done using a Bruker Avance III 400 spectrometer operating at a $^1$H Larmor frequency of 400.03 MHz
 equipped with a standard 4~mm CP-MAS HXY probe. The set up of the R-PDLF experiment was the following
 (using the notation from figures 1c and 2c in the original publication describing the R-PDLF experiment \cite{dvinskikh04}).
 The magic angle spinning (MAS) frequency used was 5.15 kHz. The recoupling pulses in the R18 blocks had
@@ -396,10 +343,10 @@ \subsection{Measurements of acyl chain order parameters}
 pulses where used giving a spectral width of 2.6~kHz in the indirect dimension and a total number of 32 points in
 the indirect dimension were recorded. These settings enable to record dipolar slices with a C--H bond order parameter
 resolution of $\pm$0.01. The C--H bond order parameter determined from a given dipolar
-splitting, $\Delta\nu$ (see e.g. Fig. \ref{R-PDLFslices} in \todo{Is this the correct figure?}) is equal to $\Delta\nu/(0.315\times21.5 kHz)$, where 0.315 is
+splitting, $\Delta\nu$ (see e.g. Fig.~\ref{R-PDLFslices} in supplementary information) is equal to $\Delta\nu/(0.315\times21.5 kHz)$, where 0.315 is
 the scaling factor of the R18 recoupling sequence and 21.5 kHz is the maximum $^1$H-$^{13}$C dipolar coupling for a C--H bond.
-The refocused-INEPT transfer \cite{morris79,burum80} %[G. Morris and R. Freeman, J. Am. Chem. Soc. 101, 760 (1979);
-was used for transferring the polarization from $^1$H nuclei to the covalently bond $^{13}$C nuclei with the delays $\tau_1 = 1.94$~ms and $\tau_2 = 0.97$~ms
+The refocused-INEPT transfer \cite{morris79,burum80} 
+was used for transferring the polarization from $^1$H nuclei to the covalently bond $^{13}$C nuclei with the delays of $\tau_1 = 1.94$~ms and $\tau_2 = 0.97$~ms
 (set as multiples of the MAS rotation period). The pulses for the refocused-INEPT sequence had a nutation frequency equal to 63.45~kHz.
 For acquiring the spectra, a total number of 1024 transients were recorded for each point in the indirect dimension, using an acquisition
 time of 0.1~s under SPINAL64 $^1$H decoupling \cite{fung00} with a nutation frequency of 50~kHz, and with dwell time giving a spectral
@@ -407,7 +354,14 @@ \subsection{Measurements of acyl chain order parameters}
 described e.g. in Ref.~\citenum{ferreira08}. The dipolar splittings in the crowded spectral region
 between 29 and 30 ppm were assigned based on the previous assignments for POPC \cite{ferreira13} 
 and the POPS order parameters calculated from simulations in this work.
- 
+
+As in our previous work~\cite{NMRlipidsIV}, the sample was prepared by first mixing POPS powder
+(1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, purchased from Avanti Polar Lipids as sodium salt)
+with water (lipid:water 60:40 wt-\%) in an Eppendorf tube. The mixture was repeatedly centrifuged and
+stirred (approximately 5 to 6 times) until a homogeneous viscous fluid was visually observed.
+Then 20 mg of the sample was transferred to an NMR insert suitable for 4 mm NMR rotors.
+Experiments were done at 298~K.
+
 \subsection{Simulation details} 
 
 
@@ -419,7 +373,7 @@ \subsection{Simulation details}
            added buffer concentrations,
            amounts of individual molecules,
            and the deployed models.
-           The fatty acid chains for all lipids are palmitoyl (sn-1) and oleoyl (sn-2).
+           The fatty acid chains for all lipids are palmitoyl ({\it sn}-1) and oleoyl ({\it sn}-2).
          }\label{tbl:sim-list}
 \begin{tabular}{r  l | r r r r | r r | c c }
    \multicolumn{1}{r}{PC:PS} & \multicolumn{1}{l}{ }  &  \multicolumn{4}{c}{added buffer conc. / mM}    & \multicolumn{2}{c}{no. molecules} &  \multicolumn{2}{c}{simulated with}  \\
@@ -459,12 +413,12 @@ \subsection{Simulation details}
 were performed in an orthorhombic simulation box with periodic boundary conditions
 using the GROMACS 2018 \cite{Abraham15} simulation package. 
 The simulated systems are listed in Table~\ref{tbl:sim-list}
-and the used simulation parameters in Table~\ref{tbl:mdpar}. 
-All simulations were ran for a minimum of $1 \, \mu$s,
+and the used simulation parameters in Table~\ref{tbl:mdpar} in supplementary information. 
+All simulations were ran for a minimum of $1 \, \mu$s at 298 K,
 and the first  $50 \,$ns were omitted as an equilibration period. 
-For deposited trajectories and parameter files see 
+Generated trajectories and parameter files are available from 
 Refs.~\citenum{ecclipids_pcps_nacl_kcl_series, ecclipids_pcps_cacl2_series, ecclipids_pcps_mixtures_counterions, 
-               lipid17_nacl_kcl_series, lipid17_ff99_ions, lipid17_cacl_series}
+               lipid17_nacl_kcl_series, lipid17_ff99_ions, lipid17_cacl_series}. 
 
 In the reference simulations with the standard Amber force field,
 the Lipid14 parameters~\cite{dickson14} for POPC, the Lipid17 parameters for POPS \cite{lipid17-future},
@@ -473,46 +427,31 @@ \subsection{Simulation details}
 The Lipid17 parameters for POPS were obtained from AmberTools18 \cite{amber18} 
 and converted to Gromacs format using acpype \cite{acpype}.  
 The ion model by Dang and coworkers~\cite{smith94,chang1999,dang2006} was used with Amber lipids because
-the default Amber ion parameters \cite{aqvist90} led to the artificial clustering of ions in solution \cite{NMRlipidsIV}.
-In the ECC-lipids simulations,
+the default Amber ion parameters, derived by {\AA}qvist \cite{aqvist90}, led to the artificial clustering of ions in solution \cite{NMRlipidsIV}.
+
+In the ECC-lipids simulations, we used
 the ECC-POPC parameters~\cite{melcr18} (available from Ref. \citenum{ECC-POPC_nacl_cacl2_files}), 
-the ECC-POPS parameteres derived in this work (see above), 
-the SPC/E~\cite{Berendsen1987} water model, and ECC-ions \cite{martinek17, kohagen16, Pluharova2014} were used.
+the ECC-POPS parameteres derived in this work (see above for details and Ref. \citenum{ecclipids_pcps_nacl_kcl_series} for parameters), 
+the SPC/E~\cite{Berendsen1987} water model, and ECC-ions \cite{martinek17, kohagen16, Pluharova2014}. 
 The SPC/E water model was selected because its lower dielectric constant is consistent with the
 ECC concept \cite{leontyev11,leontyev14}.
-\begin{table}[tbp]
-  \caption{Simulation parameters}
-  \label{tbl:mdpar}
-  \begin{tabular}{ll}
-    simulation property & parameter   \\
-    \hline
-    time-step           & 2~fs         \\
-    equilibration time  & 50~ns  \\
-    total simulation time     & $\geq 1 \mu$s  \\
-    temperature         & 298~K       \\
-    thermostat          & v-rescale  \cite{bussi07}   \\
-    barostat            & Parrinello-Rahman, semi-isotropic \cite{parrinello81} \\
-    long-range electrostatics & PME  \cite{darden93}  \\
-    cut-off scheme      & Verlet \cite{Pall13}      \\
-    Coulomb and VdW cut-off & 1.0~nm \\
-    constraints         & LINCS, only hydrogen atoms \cite{hess97} \\
-    constraints for water & SETTLE  \cite{miyamoto92} \\
-    \hline
-  \end{tabular}
-\end{table}
+
  
-The C--H bond order parameters were calculated directly from Eq.~\ref{OPequation}.
+The C--H bond order parameters were calculated directly from Eq.~\ref{OPequation}
+using a Python code openly available at Ref.~\citenum{MATCHgit} ({\tt scripts/calcOrderParameters.py}) 
+that uses the MDAnalysis library \cite{agrawal11,gowers16}.  
 The time average was first calculated for each lipid, and
 the standard error of the mean from these individual values was then used as the
 error estimate \cite{botan15,ollila16,NMRlipidsIV}.
-Python program that uses the
-MDAnalysis library \cite{agrawal11,gowers16} is available in Ref.~\citenum{MATCHgit} ({\tt scripts/calcOrderParameters.py}). 
 The ion number density profiles were calculated using the {\tt gmx density} tool
 of the Gromacs sofware package \cite{gromacsMANUAL}.
-The salt concentrations in buffer before solvating the lipids, reported in the used experimental data set \cite{roux90},
+The salt concentrations in a buffer before solvating the lipids, 
+as reported in the used experimental data set \cite{roux90},
+%is simulations
 were calculated as $[{\rm salt}]=N_{\rm c} \times[{\rm water}]\,/\,N_{\rm w}$,
-where $N_{\rm c}$ is the number of cations in simulation, $[{\rm water}]$\,=\,55.5~M and $N_{\rm w}$
-is the number of water molecules in the simulation.
+where $N_{\rm c}$ is the number of additional cations, 
+$N_{\rm w}$ is the number of water molecules,
+and $[{\rm water}]$\,=\,55.5~M. 
 As discussed in our previous work \cite{NMRlipidsIV}, the hydration levels of
 multilamellae are expected to be sufficiently similar in the used simulations and reference experiments \cite{roux90}.
 
@@ -531,22 +470,24 @@ \subsection{ECC-POPS improves agreement in experimental structural parameters of
 can be directly calculated from MD simulations~\cite{ollila16}.
 The X-ray scattering form factors and C-H bond order parameters in
 the headgroup and glycerol backbone region of a POPS lipid bilayer are already available in the literature \cite{kucerka14,NMRlipidsIV}.
-Here, we measure also the C--H bond order parameters of the acyl chain region from a sample of POPS multi-lamellar vesicles by means of a $^1$H--$^{13}$C dipolar recoupling 2D NMR experiment. More specifically, as described in detail in the Methods section, we performed R-PDLF 2D spectroscopy~\cite{dvinskikh04} to obtain spectra correlating chemical shifts (direct dimension) and C--H bond dipolar couplings (indirect dimension) from which the C--H bond order parameters defined in eq.~\ref{OPequation} can be determined. The assignment of the peaks in the $^{13}$C chemical shift dimension to acyl chain carbon sites was done based on previous work {\cite{ferreira13}} and is shown in Figs.~\ref{INEPT}~and~\ref{R-PDLF}. The dipolar splittings for the assigned carbons that were used to calculate their C--H bond order parameter magnitudes are shown in Fig.~\ref{R-PDLFslices}. Because the complete assignment of the peaks in the crowded spectral region between 29-31 ppm was not possible due to the chemical shift overlap of different carbons (~\ref{R-PDLF}), we partially assigned the acyl chain order parameters of this region to mimic the profile predicted by the MD simulations (Fig.~\ref{simVSexpNOions_POPS}).
+Here, we measure also the C--H bond order parameters of the acyl chain region from multi-lamellar POPS vesicles using $^1$H--$^{13}$C
+dipolar recoupling 2D NMR spectroscopy. As described in the Methods section, we performed R-PDLF 2D spectroscopy~\cite{dvinskikh04} to
+obtain a spectra correlating chemical shifts (direct dimension) and C--H bond dipolar couplings (indirect dimension) from which the C--H bond order parameters defined in eq.~\ref{OPequation} can be determined. The assignment of the peaks in the $^{13}$C chemical shift dimension to acyl chain carbon sites was done based on previous work {\cite{ferreira13}} and is shown in Figs.~\ref{INEPT}~and~\ref{R-PDLF}. The dipolar splittings for the assigned carbons that were used to calculate their C--H bond order parameter magnitudes are shown in Fig.~\ref{R-PDLFslices}. Because the complete assignment of the peaks in the crowded spectral region between 29-31 ppm was not possible due to the chemical shift overlap of different carbons (Fig.~\ref{R-PDLF}), we partially assigned the acyl chain order parameters of this region to mimic the profile predicted by the MD simulations (Fig.~\ref{simVSexpNOions_POPS}).
 
 
 \begin{figure}[tb!] 
   \centering 
-  \includegraphics[width=\figwidth]{../img/ecc_pops/Order-parameters_form-factors_exp-L17-ECC-lipids.pdf}
-  \includegraphics[width=\figwidth]{../img/POPSstructure.pdf} 
+  \includegraphics[width=3.33in]{../img/formF_OPs_APLinset_POPSchemfig.pdf} 
 \hfill
   \caption{\label{simVSexpNOions_POPS} 
-    \textbf{Top:} X-ray scattering form factors from simulations with Lipid17/Dang \citep{lipid17-future, dang2006} and 
+    \textbf{(A)} X-ray scattering form factors and area per phospholipid of a POPS bilayer
+    from simulations with Lipid17/Dang \citep{lipid17-future, dang2006} and 
     ECC-POPS/ECC-ions \cite{martinek17, Pluhackova2016} compared with experiments~\citep{kucerka14} at 298~K. 
-    \textbf{Middle:} Order parameters of POPS head group, glycerol backbone and acyl chains  
+    \textbf{(B)} Order parameters of POPS headgroup, glycerol backbone and acyl chains  
     from the same simulations 
     compared with experiments at 298~K. \citep{NMRlipidsIV}
     Open/closed symbols are used for palmitoyl/oleoyl chains of POPS. 
-    \textbf{Bottom:} The chemical structure of POPS and the labeling of the carbon segments. 
+    \textbf{(C)} Chemical structure of POPS and labeling of carbon segments. 
   }  
 \end{figure} 
 
@@ -554,89 +495,54 @@ \subsection{ECC-POPS improves agreement in experimental structural parameters of
 The Lipid17/Dang simulation gives 
 discrepancies with the experimental X-ray form factor,
 larger acyl chain order parameters,
-and smaller area per molecule than the experimental values (Fig.~\ref{simVSexpNOions_POPS} and table~\ref{tab:apls}),
+and smaller area per molecule than the experimental values (Fig.~\ref{simVSexpNOions_POPS}),
 indicating that this simulation predicts a too compact POPS lipid bilayer. 
 The ECC-POPS simulation gives better agreement with experiments for the X-ray scattering form factors and 
 acyl chain order parameters (Fig.~\ref{simVSexpNOions_POPS}),
 indicating that the bilayer dimensions and acyl chain
 conformations are well described by the force field. The area per lipid from ECC-POPS simulation is slightly
-smaller than the value reported from SDP model \cite{kucerka14} (table~\ref{tab:apls}), but the values
-agree within their error estimates. The larger area in ECC-POPS simulation can be
+smaller than the value reported from SDP model \cite{kucerka14} (Fig.~\ref{simVSexpNOions_POPS}), but the values
+agree within their error estimates. Both the smaller order parameters and larger area in ECC-POPS compared to Lipid17/Dang simulation can be
 explained by increased headgroup repulsion due to lower counterion binding affinity (Fig. \ref{fig:POPS-counterions-dens}).
 This explains also the larger area per molecule (57~\AA$^2$) reported for Lipid17 POPS simulations
-%being closer to the experimental value, 
-with {\AA}qvist ions~\cite{NMRlipidsIV}.
-However, the Dang ions are used here to analyze the effect of ECC to the properties of a POPS lipid bilayer because
-{\AA}qvist ions produce known artifacts, like artificial aggregation of ions at larger salt concentrations \cite{kohagen16, chen07, NMRlipidsIV}.
+with {\AA}qvist ion parameters~\cite{NMRlipidsIV}.
+However, the Dang ion parameters are used here to analyze the effect of ECC to the properties of a POPS lipid bilayer because
+{\AA}qvist ion parameters produce known artifacts, like artificial aggregation of ions at larger salt concentrations \cite{kohagen16, chen07, NMRlipidsIV}.
 
-%SAMULI: I have moved this figure back to the main text
-\begin{figure}[hbp!] 
+\begin{figure}[tbp!] 
   \centering 
-  \includegraphics[width=8cm]{../img/ecc_pops/density_profiles_na-k-counterions_wat_phos_compar_purePOPS_ecclipids-lipid17.pdf}
+  \includegraphics[width=3.33in]{../img/ecc_pops/density_profiles_na-k-counterions_wat_phos_compar_purePOPS_ecclipids-lipid17.pdf}
   \caption{\label{fig:POPS-counterions-dens}
     Number density profiles of \ce{K^{+}} and \ce{Na^{+}} counterions along the membrane normal axis
     in ECC-lipids (solid lines) and Lipid17/Dang (dashed lines) simulations of pure POPS bilayers.  
     The density profiles of phosphate groups and water are divided by 4 and 100, respectively.  
   }
-  \todo{This figure might be more clear without the lipids in background.}
 \end{figure}
 
 
-
-\begin{table}[tb!] 
-\centering
-  \caption{Area per lipid of POPS bilayers, $A_L$, from simulations with different force fields at 298~K with \ce{Na^+} counterions. \label{tab:apls} } 
-  \begin{tabular}{l|c } 
-    \multicolumn{2}{c}{POPS} \\
-    model          & $A_L$ / Å$^2$    \\ 
-    \hline 
-    Lipid17/Dang              & 53.5$\pm$ 1.7   \\ 
-%    Lipid17/ff99              & 57.9$\pm$ 1.7   \\ 
-%    \hline 
-    ECC-POPS/ECC-ions         & 59.8$\pm$ 1.8   \\ 
-%    \hline 
-    experiment (SDP model) \citep{kucerka14} & 62.7$\pm$ 1.3  \\ 
-%    \hline 
-  \end{tabular} \\
-\todo{J: This table will become a small inset plot in the top of Fig.~\ref{simVSexpNOions_POPS} }
-\end{table} 
-
 Despite the success in simulating bilayer dimensions and acyl chain conformations,
 lipid force fields have typically problems in capturing the correct glycerol backbone and
 headgroup order parameters and conformations \cite{botan15,ollila16,NMRlipidsIV}.
 This is the case also for Lipid17 POPS simulations, where the headgroup and glycerol backbone
 order parameters are quite far from experimental values with Dang (Fig.~\ref{simVSexpNOions_POPS}),
-{\AA}qvist and Joung-Cheatham ions~\cite{NMRlipidsIV}. The values from ECC-POPS simulation are closer,
+{\AA}qvist and Joung-Cheatham ion parameters~\cite{NMRlipidsIV}. The values from ECC-POPS simulation are closer,
 but not in full agreement with experiments (Fig.~\ref{simVSexpNOions_POPS}).
 
-
-% SAMULI: I commented this out to simplify the manuscript
-%
-%Especially, the experimentally observed more negative values of the $\beta$-carbon
-%and the larger forking (difference of order parameters between hydrogens attached to the
-%same carbon \cite{ollila16}) of the $\alpha$-carbon in POPS than in POPC \cite{NMRlipidsIV}
-%are not reproduced by neither of the models here. 
-%These differences are previously related
-%to a more rigid structure of PS headgroup \cite{browning80,buldt81} and 
-%the stiffness of the C$_\alpha$-C$_\beta$-C$_\gamma$-O$_\gamma$ dihedral \cite{NMRlipidsIV}
-%plotted in Fig.~\ref{fig:dihedral}. 
-%Interestingely, this dihedral angle is more flexible in ECC-POPS compared to Lipid17 
-%suggesting that its rigidity is overestimated in Lipid17 due to the lack of electronic polarizability,
-%while the same dihedral parameters yield too small forking in ECC-POPS.
-
 In conclusion, the stuctural quality of ECC-POPS is similar to the other currently available
-lipid force fields \cite{botan15, catte16, Pluhackova2016, nmrlipids_proj4},
+lipid force fields \cite{botan15, catte16, Pluhackova2016,NMRlipidsIV},
 giving good agreement with experiments for acyl chain conformations and bilayer dimensions,
 while there is a room for improvement in the glycerol backbone and headgroup region
 conformations.
  
-\subsection{Binding of counterions to POPS and POPC and interactions between their head groups}
+\subsection{Binding of counterions to POPS and POPC and interactions between their headgroups}
 Binding affinity of monovalent ions to lipid bilayers depends strongly on
 force field parameters in simulations \cite{catte16,NMRlipidsIV}.
 The cation binding affinities to lipid bilayers in simulations have been previously evaluated
 against experiments using the order parameters of $\alpha$ and $\beta$ carbons in the
-phosphatidylcholine (PC) lipid headgroup (see Fig.~\ref{fig:delta_ordPar_NaCl_PC-PS_mix_PC} for the labeling) \cite{catte16,melcr18,NMRlipidsIV},
-which decrease proportionally to the bound charge according to the ''electrometer concept'' \citep{seelig87}.
+phosphatidylcholine (PC) lipid headgroup (see Fig.~\ref{fig:delta_ordPar_monoval_PCPS} for the labeling) \cite{catte16,melcr18,NMRlipidsIV}.
+According to the ''electrometer concept'' \citep{seelig87}, these order parameters
+decrease proportionally to the amount of bound positive charge because the headgroup dipole tilts more
+parallel to the membrane normal.
 Although the response of PS lipid headgroup order parameters to the bound charge is also systematic,
 it is less well undestood and the addition of cations may cause phase transitions in negatively charged
 bilayers \cite{feigenson86,mattai89,roux91,roux90}.
@@ -647,29 +553,26 @@ \subsection{Binding of counterions to POPS and POPC and interactions between the
 Because the evaluation of monovalent ion binding affinity to bilayers with
 PS lipids is complicated by the lack of ion-free state (counterions are always present with negatively charged lipids),
 we evaluate the counterion binding affinity to POPC:POPS mixtures also by monitoring
-the response of POPC headgroup order parameters to the increasing mole fraction of PS lipids~\cite{NMRlipidsIV}.
+the response of POPC headgroup order parameters to the increasing molar fraction of PS lipids~\cite{NMRlipidsIV} 
+(Fig.~\ref{fig:delta_ordPar_NaCl_PC-PS_mix_PC}).
 
 \begin{figure}[tbp!] 
   \centering 
-  \includegraphics[height=\figheightsmall]{../img/ecc_pops/order_parameters_changes_ecc-lip_L14_A-B-PN-COO_POPC_kcl.pdf} 
-  \includegraphics[height=\figheightsmall]{../img/ecc_pops/order_parameters_changes_ecc-lip_L14_A-B-PN-COO_POPC_nacl.pdf} 
-  \includegraphics[height=\figheightsmall]{../img/ecc_pops/order_parameters_changes_ecc-lip_L14_A-B-PN-COO_POPS_kcl.pdf} 
-  \includegraphics[height=\figheightsmall]{../img/ecc_pops/order_parameters_changes_ecc-lip_L14_A-B-PN-COO_POPS_nacl.pdf} 
+  \includegraphics[width=\figwidthfull]{../img/deltaOP_nacl_kcl_PC-PS.pdf} 
   \caption{\label{fig:delta_ordPar_monoval_PCPS}
-    Changes of the head group order parameters, and the angles of P--N and ${\rm{C}}_\beta-{\rm{C}}_\gamma$ (stars) vectors
-    with respect to the membrane normal of POPC (left) and POPS (right) in a POPC:POPS (5:1) bilayer 
+    Changes of the headgroup order parameters, and the angles of P--N and ${\rm{C}}_\beta-{\rm{C}}_\gamma$ (stars) vectors
+    with respect to the membrane normal of POPC (A, B) and POPS (C, D) in a POPC:POPS (5:1) bilayer 
     as a function of \ce{KCl} and \ce{NaCl} concentration from ECC-lipids and Lipid17/Dang simulations 
-    compared with experimental values from Ref. \citenum{roux90} (signs from Ref. \citenum{ferreira16}) at 298 K.
-    The y-axis for the $\alpha$-carbon results of POPS (middle right) is transferred
+    compared with experimental values from Ref. \citenum{roux90} (signs from Refs.~\citenum{ferreira16} and~\citenum{NMRlipidsIV}) at 298 K.
+    Because experimental data with \ce{NaCl} is not available for POPC, the data for KCl and \ce{LiCl} (B, dashed lines)
+    are shown as lower and upper bounds, respectively, for the response to \ce{NaCl}. 
+    The y-axis for the $\alpha$-carbon results of POPS (C and D, middle) is shifted
     with the same value for both order parameters such that the lower order
     parameter value from pure POPS is at zero to correctly illustrate the significant forking.
-    Because experimental data with \ce{NaCl} is not available for POPC, the data for KCl and \ce{LiCl} (dashed line, left)
-    are shown as lower and upper bounds, respectively, for the response to \ce{NaCl}. Error bars are not visible for ECC-lipids simulations because they are smaller than the point size.}
-\todo{J: Will improve this figure with panels A, B, C and D 
-and put POPC together, POPS together 
-and remove the duplicate y-axis titles 
-and make a common legend distinguishing different experiments better. } \\
-\todo{The scale in left and right columns (response to KCl and NaCl) should be the same (not necessarily the same scale for POPC and POPS though).}
+    Error bars are not visible for ECC-lipids simulations because they are smaller than the point size.
+    Inset in A shows the labeling of carbon segments in a POPC headgroup.
+    For the ion density profiles, see Fig. \ref{fig:nacl-dens_PCPS} in supplementary information.
+  }
 \end{figure} 
 
 
@@ -677,14 +580,13 @@ \subsection{Binding of counterions to POPS and POPC and interactions between the
 while the decrease was more pronounced with Li$^+$ ions and was strongest with divalent Mg$^{2+}$ and Ca$^{2+}$ ions~\cite{roux90},
 suggesting that the binding affinity increases in order K$^{+}$ $<$ Li$^{+}$  $<$ Mg$^{2+}$  $<$ Ca$^{2+}$.
 The small changes of POPC headgroup order parameters with increasing amount of KCl are close to experiments
-%and the change in P--N vector is negligible
-in both force fields (Fig.~\ref{fig:delta_ordPar_monoval_PCPS}).
+in both force fields (Fig.~\ref{fig:delta_ordPar_monoval_PCPS} A).
 The slightly overestimated change of the $\alpha$-carbon
 order parameter in the Lipid17/Dang simulations may be due to the
-deeper penetration of \ce{K+} into the bilayer (Fig.~\ref{fig:delta_ordPar_NaCl_PC-PS_mix_PC}).
+deeper penetration of \ce{K+} into the bilayer (Fig.~\ref{fig:delta_ordPar_NaCl_PC-PS_mix_PC} A).
 Experimental data with the additional amount of \ce{Na+} in POPC:POPS (5:1) mixture is not available,
 but \ce{Li+} and \ce{K+} results give the lower and the upper bounds, respectively, to the sodium binding
-affinity (Fig.~\ref{fig:delta_ordPar_monoval_PCPS}). In ECC-lipids simulations,
+affinity (Fig.~\ref{fig:delta_ordPar_monoval_PCPS} B). In ECC-lipids simulations,
 the response of POPC headgroup order parameters to the additional sodium is close to the
 experimental results for lithium, while in Lipid17/Dang simulations the response is larger.
 Overall, the results suggest that the \ce{Na+} binding affinity is
@@ -692,195 +594,143 @@ \subsection{Binding of counterions to POPS and POPC and interactions between the
 while the binding affinity of potassium is better described by both force fields.
 This conclusion is also supported by the POPC headgroup responses to the
 increasing amount of POPS in different simulations (Fig~\ref{fig:delta_ordPar_NaCl_PC-PS_mix_PC}).
-In experiments, the head group order parameters of PC lipids increase upon addition of
+In experiments, the headgroup order parameters of PC lipids increase upon addition of
 negatively charged PS lipids, as predicted by the electrometer concept~\cite{seelig87,scherer87}.
 This is the case also in simulations with the exception of
 Lipid17/Dang with \ce{Na+} counterions, where the stronger counterion binding affinity
 cancels the influence of negatively charged lipids and the increase in PC headgroup
-order parameters is not observed.% \cite{NMRlipidsIV}.
+order parameters is not observed.
 
 \begin{figure*}[!tbp] 
   \centering 
-  \includegraphics[height=\figheightsmall]{../img/ecc_pops/density_profiles_na-k-counterions_wat_phos_compar_5PC-1PS_ecclipids-lipid17.pdf}
-  \includegraphics[height=\figheightsmall]{../Fig/order_parameters_changes_A-B_PC-PS_mix_POPC_nacl.pdf} 
-  \includegraphics[height=\figheightsmall]{../Fig/order_parameters_changes_A-B_PC-PS_mix_POPC_kcl.pdf} 
-  \includegraphics[height=\figheightsmall]{../img/POPCstructure.pdf} 
+  \includegraphics[width=\figwidthfull]{../img/deltaOP_mix_PC-PS.pdf} 
   \caption{\label{fig:delta_ordPar_NaCl_PC-PS_mix_PC} 
-    \textbf{Left:} Number density profiles of \ce{K^{+}} and \ce{Na^{+}} counterions along the membrane normal axis
+    \textbf{(A)} Number density profiles of \ce{K^{+}} and \ce{Na^{+}} counterions along the membrane normal axis
     in ECC-lipids (solid lines) and Lipid17/Dang (dashed lines) simulations of POPC:POPS (5:1) bilayers.  
     The density profiles of phosphate groups and water are divided by 4 and 100, respectively.  
-    \textbf{Middle:} The POPC head group order parameters and the P--N vector angle
+    \textbf{(B, C)} The POPC headgroup order parameters and the P--N vector angle
     with respect to the membrane normal as a function of POPS content in a bilayer
-    from ECC-lipids and Lipid17/Dang simulations with \ce{Na^+} (left) and \ce{K^+} (right) counterions.
-    Experimental order parameter values are from Ref. \citenum{scherer87}
-    and the signs from Ref. \citenum{ferreira16} 
-    (only \ce{Na^+} counterions, but shown also in the right plots for \ce{K+}).
+    from ECC-lipids and Lipid17/Dang simulations with \ce{K^+} (B) and \ce{Na^+} (C) counterions.
+    Experimental order parameter values with \ce{Na^+} are from Ref. \citenum{scherer87}
+    and the signs from Ref.~\citenum{ferreira16}. Because experimental values with \ce{K^+} are
+    not available, the data with \ce{Na^+} is shown with dashed lines in (B).
     Error bars are not visible for most of the simulation points because they are smaller than the point size.
-    \textbf{Right:} Chemical structure and labelling of carbon segments of POPC. 
+    Chemical structure and labelling of carbon segments of POPC is shown in Fig.~\ref{fig:delta_ordPar_monoval_PCPS}. 
   }
-\todo{J: Will manually improve this figure with panels A, B, C and D 
-and will erase the duplicate y-axis description 
-and will add ticks to the right side of the plotting area. } \\
-\todo{The scales should be the same in the left and right panel.}
 \end{figure*} 
 
 The behaviour of POPS headgroup can be further characterized by monitoring its order parameters in different
-lipid mixtures and ionic conditions~\cite{NMRlipidsIV,roux90}.
-In experiments, the headgroup order parameters of POPS are almost unchanged upon increasing the POPC content or monovalent ion concetration
-(\ref{fig:delta_ordPar_NaCl_PC-PS_mix_PS} and Figs.~\ref{fig:delta_ordPar_monoval_PCPS}).
-In Lipid17/Dang simulations, the changes of POPS headgroup order parameters with increasing amount of
-both POPC or monovalent salts (\ce{KCl} and \ce{NaCl}) are overestimated (\ref{fig:delta_ordPar_NaCl_PC-PS_mix_PS} and Figs.~\ref{fig:delta_ordPar_monoval_PCPS}).
-Similar results also for other force fields are reported elsewhere~\cite{NMRlipidsIV}.
+lipid mixtures and ionic conditions (Figs.~\ref{fig:delta_ordPar_monoval_PCPS} and \ref{fig:delta_ordPar_NaCl_PC-PS_mix_PS})~\cite{NMRlipidsIV,roux90}.
+In experiments, the headgroup order parameters of POPS are almost unchanged upon increasing the POPC content or monovalent ion concentration, 
+while in Lipid17/Dang simulations the changes of POPS headgroup order parameters with increasing amount of
+both POPC or monovalent salts (\ce{KCl} and \ce{NaCl}) are overestimated 
+(Figs.~\ref{fig:delta_ordPar_monoval_PCPS} and \ref{fig:delta_ordPar_NaCl_PC-PS_mix_PS}).
+Similar results are reported also for other force fields. \cite{NMRlipidsIV}
 In ECC-lipids simulations, the response of POPS headgroup order parameters to both POPC and monovalent salt concentration (\ce{KCl} and \ce{NaCl})
-are more modest and closer to experiments (\ref{fig:delta_ordPar_NaCl_PC-PS_mix_PS} and Figs.~\ref{fig:delta_ordPar_monoval_PCPS}).
+are more modest and closer to experiments. 
 The changes in order parameters can be related to the orientations of the P--N and C$_{\beta}$--C$_{\gamma}$
 vectors in POPC and POPS, which change much less and more systematically in ECC-lipids
-than in Lipid17/Dang simulations (\ref{fig:delta_ordPar_NaCl_PC-PS_mix_PS} and Figs.~\ref{fig:delta_ordPar_monoval_PCPS}). 
+than in Lipid17/Dang simulations 
+(Figs.~\ref{fig:delta_ordPar_monoval_PCPS} and \ref{fig:delta_ordPar_NaCl_PC-PS_mix_PS}).
 
-We estimate the influence of negatively charged POPS on the counterion binding affinity
+We quantify the influence of negatively charged POPS on the counterion binding affinity
 by comparing the relative surface excesses with respect to water, $\Gamma ^{w} _{\rm ion}$,
-between POPC:POPS (5:1) mixture and pure POPC in ECC-lipids simulations with the most realistic
+between POPC:POPS (5:1) mixture and pure POPC in ECC-lipids simulations with currently the most realistic
 cation binding affinities~\cite{melcr18}.
-%Threshold for counting bound \ce{Ca^{2+}} cations to a membrane
-%was set to $0.3\,\mathrm{nm}$ from oxygen atoms in lipids as in Ref.~\citenum{melcr18}.  
-%Such a quantity compares the adsorption of ions to the adsorption of water molecules at an interface 
-%without the necessity of defining a Gibbs dividing surface. \citep{melcr18, chattorajBOOK}
 The value of $\Gamma ^{w} _{\rm Na}=-0.11 \pm 0.01 \mathrm{nm}^{-2}$ for 1~M sodium in pure ECC-POPC
 simulation was reported in the previous work \cite{melcr18}.
 The presence of $\sim$17\% POPS in a POPC bilayer increases the
 value to $\Gamma ^{w} _{\rm Na}=0.092 \pm 0.005 \mathrm{nm}^{-2}$ 
 for 0.621 M sodium, while value for potassium remains negative,
 $\Gamma ^{w} _{\rm K}=-0.123 \pm 0.005 \mathrm{nm}^{-2}$ in POPC:POPS (5:1) mixture (Fig.~\ref{fig:nacl-dens_PCPS}).
-As discussed above, the sodium binding to POPC:POPS (5:1) mixture may be slightly overestimated also in
-ECC-lipids simulations. The response of headgroup order parameters to the addition of NaCl are
-slightly overestimated also in ECC-POPC simulations (Fig 3 in Ref. \citenum{melcr18}),
-suggesting that similar small overestimation of sodium binding may also occur to a pure POPC bilayer.
-Therefore, the overestimation may arise from the sodium interactions with PC headgroup and
-increase in binding affinity due to PS lipids would not be affected.
+The increase in sodium binding affinity upon addition of anionic POPS is not expected to depend on
+the slightly overestimated \ce{Na+} binding in ECC-lipid simulations, because the
+inaccuracy is similar for pure POPC (Fig~3 in Ref.~\citenum{melcr18}) and POPC:POPS (5:1) mixture (Fig. \ref{fig:delta_ordPar_monoval_PCPS}).
+
 
 \subsection{Molecular interaction and binding affinity of \ce{Ca^{2+}} cations to mixed POPC:POPS (5:1) membrane} 
 \label{section:lip-ion_ca}
 Our recent work demonstrates that the POPC headgroup order parameters measured
 from POPC:POPS (5:1) mixture as a function of CaCl$_2$ concentration 
-can be used to evaluate the calcium binding affinity to lipid bilayers containing PS lipids \cite{roux90, NMRlipidsIV}.
+can be used to evaluate the calcium binding affinity to lipid bilayers containing PS lipids \cite{roux90,NMRlipidsIV}.
 The decrease of the PC headgroup order parameters in this mixture upon addition of \ce{CaCl2} 
 were overestimated by the Lipid17/Dang simulations (Fig.~\ref{fig:delta_ordPar_CaCl_PCPS})
-and all other tested force fields except CHARMM36 with the recently introduced NBfix for calcium \cite{kim16},
+and all other tested force fields except CHARMM36 with the recently introduced NBfix parameters for calcium \cite{kim16,han2018graph},
 which underestimated the headgroup order parameter response.
-In ECC-lipids simulations, the headgroup responses are in better agreement with experiments (Fig.~\ref{fig:delta_ordPar_CaCl_PCPS}),
+In ECC-lipids simulations, the headgroup responses are in better agreement with experiments,
 indicating that the lower binding affinity than in Lipid17/Dang simulations is more realistic (Fig.~\ref{fig:cacl-dens_PCPS}).
-Therefore, we use ECC-lipids simulations to estimate the influence of negative charged POPS on
+Therefore, we use ECC-lipids simulations to quantify the influence of negatively charged POPS on
 calcium binding affinity to lipid bilayers.
 The relative surface excess of calcium with respect to water 
-%  previously we used 350mM conc, but I think it is better to compare to a higher concentration to support the whole argument bullet-proof
-%  $\Gamma^{w}_{Ca} = 0.06\mathrm{nm^{-2}}$ ($\sim ?.?$ phospholipids per bound \ce{Ca^{2+}}) for pure POPC bilayer with 346~mM CaCl$_2$ \cite{melcr18, ECC-POPC_nacl_cacl2_files} 
-$\Gamma^{w}_{Ca} = 0.09\mathrm{nm^{-2}}$ ($\sim 5.4$ phospholipids per bound \ce{Ca^{2+}}) for pure POPC bilayer with 467~mM CaCl$_2$ \cite{ECC-POPC_nacl_cacl2_files}
+$\Gamma^{w}_{Ca} = 0.09\mathrm{nm^{-2}}$
+for pure POPC bilayer with 467~mM CaCl$_2$ \cite{ECC-POPC_nacl_cacl2_files}
 is increased to
-$\Gamma^{w}_{Ca} = 0.24\mathrm{nm^{-2}}$ ($\sim 4.8$ phospholipids per bound \ce{Ca^{2+}}) for the POPC:POPS (5:1) bilayer with 409 mM CaCl$_2$.
+$\Gamma^{w}_{Ca} = 0.24\mathrm{nm^{-2}}$
+for the POPC:POPS (5:1) bilayer with 409 mM CaCl$_2$.
+At these concentrations, the total amount of lipids per bound \ce{Ca^{2+}} is
+$\sim 5.4$ in the pure POPC system and $\sim 4.8$ in the POPC:POPS (5:1) mixture.
+Also, the residence times of \ce{Ca^{2+}} at the membrane 
+are 3-4 times longer in POPC:POPS (5:1) mixture (Fig.~\ref{fig:hist_residence_times}) than in pure POPC \cite{melcr18}.
 Besides lower binding affinity, ECC-lipids simulations yield smaller error bars for order parameters and shorter residence times (Fig.~\ref{fig:hist_residence_times}) 
 than those typically observed in simulations with other force fields \cite{javanainen17,melcr18,NMRlipidsIV},
 suggesting that the ECC accelerates the equilibration of ions at lipid bilayer interface.
-Therefore, our 1 $\mu$s simulations seem to be sufficiently long for the ECC-lipids simulations, because
+Therefore, our 1 $\mu$s simulations are sufficiently long for the ECC-lipids simulations, because
 90\% of the calcium residence times are shorter than $60\,\mathrm{ns}$ for pure POPC bilayer
 and shorter than $200\,\mathrm{ns}$ for POPC:POPS (5:1) mixture, while the
 longest observed residence times are $141\,\mathrm{ns}$ and $485\,\mathrm{ns}$, respectively (Fig.~\ref{fig:hist_residence_times}).
-Interestingly, the calcium residence times are 3-4 times longer in POPC:POPS (5:1) mixture than in pure POPC.
+
 
 
 \begin{figure}[tbp!] 
   \centering 
   \begin{tabular}{ c }
-  \includegraphics[height=1.5\figheightsmall]{../img/ecc_pops/density_profiles_ca_na_k_cl_wat_phos_ecclipids_lipid17_compar_80and200mMCaCl2.pdf}
-  \includegraphics[height=1.5\figheightsmall]{../img/ecc_pops/order_parameters_changes_ecc-lip_L14_A-B-PN-COO_POPC_cacl.pdf} 
-  \includegraphics[height=1.5\figheightsmall]{../img/ecc_pops/order_parameters_changes_ecc-lip_L14_A-B-PN-COO_POPS_cacl.pdf} 
+  \includegraphics[width=\figwidthfull]{../img/deltaOP_cacl_PC-PS.pdf} 
   \end{tabular}
-%  \begin{tabular}{ c }
-%  \includegraphics[width=3cm]{../img/bound_ca_populations.pdf} \\
-%  \includegraphics[width=3cm]{../img/stoichiometry_CaCl2_comparison_Ecc-lipids_PC-vs-PCPS.pdf} 
-%  \end{tabular}
-  \caption{\label{fig:cacl-dens_PCPS} 
-    \textbf{Left panel:}
+  \caption{
+    \label{fig:cacl-dens_PCPS} 
+    \label{fig:delta_ordPar_CaCl_PCPS} 
+    \textbf{(A)}
     Number density profiles of \ce{Ca^{2+}} and \ce{Cl^-} ions and \ce{Na^{+}} counterions 
-    along the normal of the membrane starting at the centre
-    for the negatively charged membrane with the composition 5\,PC:1\,PS
-    at 80~mM (top) and 200~mM (bottom) added buffer concentrations of \ce{CaCl2} from simulations with ECC-lipids (solid) and Lipid17 (dashed). 
-    In order to visualize the density profiles with a comparable scale 
-    the density profile of~\ce{Ca^{2+}} ions are divided by 2, and 
-    the density profiles of phosphate groups and water are divided by 4 and 100, respectively.  
-  }
-  \caption{\label{fig:delta_ordPar_CaCl_PCPS} 
-    \textbf{Middle panels:}
-    Changes of the head group order parameters, and the angles of P--N (circles) and C$_\beta$--C$_\gamma$ (stars) vectors 
-    with respect to the membrane normal of POPC (left) and POPS (right) in a POPC:POPS (5:1) bilayer 
-    as a function of \ce{CaCl$_2$} concentration from ECC-lipids and Lipid17/Dang simulations 
+    along the normal of POPC:POPS (5:1) bilayer with 80~mM (A, top) and 200~mM (A, bottom)
+    of \ce{CaCl2} from simulations with ECC-lipids (solid) and Lipid17 (dashed). 
+    The~\ce{Ca^{2+}}, phosphate and water densities are divided by 2, 4 and 100, respectively.  
+    \textbf{(B, C)}
+    Changes of the headgroup order parameters, and the angles of P--N (circles) and C$_\beta$--C$_\gamma$ (stars) vectors 
+    with respect to the membrane normal of POPC (B) and POPS (C) in a POPC:POPS (5:1) bilayer 
+    as a function of \ce{CaCl$_2$} from ECC-lipids and Lipid17/Dang simulations 
     compared with experimental values from Ref. \citenum{roux90} (signs from Refs. \citenum{ferreira16} and \citenum{NMRlipidsIV}) at 298 K.
-    The y-axis for the $\alpha$-carbon results of POPS (middle right) is transferred
+    The y-axis for the $\alpha$-carbon results of POPS (C, right) is shifted
     with the same value for both order parameters such that the lower order
     parameter value from pure POPS is at zero to correctly illustrate the significant forking.
     Error bars are not visible for ECC-lipids simulations because they are smaller than the point size.
   }
-%  \caption{ \label{fig:cacl_complexes} 
-%    \textbf{Right top:} Percentages of the bound Ca$^{2+}$ 
-%    in exclusive contact with the given oxygen moiety
-%    when bound to PC only, PS only or simultaneously to both
-%    calculated from ECC-lipids simulation of POPC:POPS (5:1) bilayer with 409 mM CaCl$_2$. 
-%%	The areas represent populations of bound \ce{Ca^{2+}} 
-%%	only to the given moieties exclusively (shades of orange and red)
-%%	or their combinations (CHANGE:blue)
-%%	separately for PC, PS, or PC and PS simultaneously. 
-%%	The areas sum up to total populations at the respective lipids. %
-%	In the case of simultaneous binding to both PC and PS%,
-%	the percentages refer to the moieties in PS.
-%	% i.e., PC can interact with any considered moiety.
-%        For numerical values, see table~\ref{tab:binding}.
-%    \textbf{Right bottom:} Relative probabilities of \ce{Ca^{2+}} ions to coordinate with a certain number of lipids
-%    in pure POPC bilayer with 350 mM CaCl$_2$ and in POPC:POPS (5:1) mixture with 400 mM CaCl$_2$.  
-%    Analysis was done for both systems by considering all lipids (blue and violet) and
-%    for POPC:POPS (5:1) mixture also by considering POPC and POPS lipids separately (green and orange). 
-%    %All lipids were taken into account with the exception of the complexes in light green and orange, 
-%    %for which we counted only contacts with POPC resp POPS from the mixed 5\,PC:1\,PS negatively charged bilayer. 
-%    %The calculated probabilities of the calcium-lipid complexes also reflect only POPC (light green) resp POPS (orange). 
-%    % Probabilities were taken from simulations with comparable bulk concentrations of calcium around 250~mM. 
-%    Clusters of four or more lipids were not observed in either membrane.
-%    The threshold for counting coordinated lipids in a complex with \ce{Ca^{2+}} was set to $0.3\,\mathrm{nm}$, 
-%    as the distance between the cation and the oxygen atoms of the lipids. 
-%    Previously published simulation data \cite{melcr18} for pure POPC bilayers were taken directly from \cite{ECC-POPC_nacl_cacl2_files}. 
-%  }
-  \todo{J: Will adjust the Fig into a nice panel and change the captions accordingly. } \\
 \end{figure}
 
-% SAMULI: I separated the figure below, because it was too small to be read when combined with others.
-
 \begin{figure}[tbp!] 
   \centering 
   \begin{tabular}{ c }
-  \includegraphics[width=8cm]{../img/bound_ca_populations.pdf} \\
-  \includegraphics[width=8cm]{../img/stoichiometry_CaCl2_comparison_Ecc-lipids_PC-vs-PCPS.pdf} 
+  \includegraphics[width=\figwidthfull]{../img/populations_stoichiometry_structures.pdf} 
   \end{tabular}
   \caption{ \label{fig:cacl_complexes} 
-    \textbf{Top:} Percentages of the bound Ca$^{2+}$ 
+    \textbf{(A)} Percentages of the bound Ca$^{2+}$ 
     in exclusive contact with the given oxygen moiety
     when bound to PC only, PS only or simultaneously to both
     calculated from ECC-lipids simulation of POPC:POPS (5:1) bilayer with 409 mM CaCl$_2$. 
 	In the case of simultaneous binding to both PC and PS,
 	the percentages refer to the moieties in PS.
         For numerical values, see table~\ref{tab:binding}.
-    \textbf{Bottom:} Relative probabilities of \ce{Ca^{2+}} ions to coordinate with a certain number of lipids
-    in pure POPC bilayer with 350 mM CaCl$_2$ and in POPC:POPS (5:1) mixture with 400 mM CaCl$_2$.  
+    \textbf{(B)} Relative probabilities of \ce{Ca^{2+}} ions to coordinate with the given number of lipids
+    in a pure POPC bilayer with 350~mM~CaCl$_2$ and in POPC:POPS (5:1) mixture with 400~mM~CaCl$_2$.  
     Analysis was done for both systems by considering all lipids (blue and violet) and
-    for POPC:POPS (5:1) mixture also by considering POPC and POPS lipids separately (green and orange). 
-    %All lipids were taken into account with the exception of the complexes in light green and orange, 
-    %for which we counted only contacts with POPC resp POPS from the mixed 5\,PC:1\,PS negatively charged bilayer. 
-    %The calculated probabilities of the calcium-lipid complexes also reflect only POPC (light green) resp POPS (orange). 
-    % Probabilities were taken from simulations with comparable bulk concentrations of calcium around 250~mM. 
+    for POPC:POPS (5:1) mixture also by considering only POPC and POPS lipids separately (green and orange). 
     Clusters of four or more lipids were not observed in either membrane.
     The threshold for counting coordinated lipids in a complex with \ce{Ca^{2+}} was set to $0.3\,\mathrm{nm}$, 
-    as the distance between the cation and the oxygen atoms of the lipids. 
-    Previously published simulation data \cite{melcr18} for pure POPC bilayers were taken directly from \cite{ECC-POPC_nacl_cacl2_files}. 
+    for the distance between the cation and the oxygen atoms of the lipids. 
+    \textbf{(C and D)} Representative example configurations of \ce{Ca^{2+}} coordinated complexes 
+    of one POPS with one (C) or two POPC lipids (D). 
+    More configurations are shown in Fig.~\ref{fig:strcutures_SI} in the SI. 
+    Previously published simulation data for pure POPC bilayers \cite{melcr18} were taken directly from Ref.~\citenum{ECC-POPC_nacl_cacl2_files}. 
   }
-  \todo{Bottom: The x-axis label should be changed to ''number of lipids directly bound to Ca$^{2+}$''.
-    The current label has another meaning in the text now.} \\
-  \todo{Bottom: The labels could be more clear. Maybe ''PC in POPC:POPS(5:1)'' ...}
 \end{figure} 
 
 Interactions between Ca$^{2+}$ ions and PS lipids can be further characterized by monitoring
@@ -889,75 +739,43 @@ \subsection{Molecular interaction and binding affinity of \ce{Ca^{2+}} cations t
 on low CaCl$_2$ concentrations with a rapid saturation below 100~mM  (Fig.~\ref{fig:delta_ordPar_CaCl_PCPS}) \cite{roux90}.
 These changes are overestimated in simulations with Lipid17/Dang (Fig.~\ref{fig:delta_ordPar_CaCl_PCPS})
 and other tested force fields in our recent work \cite{NMRlipidsIV}, 
-including CHARMM36 with the NBfix correction for calcium
+including CHARMM36 with the NBfix corrections for calcium
 which underestimated the binding affinity.
 In ECC-lipids simulations, the changes of the PS headgroup order parameters are not overestimated,
-but the strong dependence on low concetrations of CaCl$_2$ is not fully reproduced (Fig.~\ref{fig:delta_ordPar_CaCl_PCPS}).
+but the strong dependence on low concentrations of CaCl$_2$ is not fully reproduced (Fig.~\ref{fig:delta_ordPar_CaCl_PCPS}).
 In addition to possibly suboptimal interactions between calcium ions and PS headgroup, the potential sources of this
-discrepancy include the above observed sligth overestimation of \ce{Na^+} counterions and
+discrepancy include the above observed slight overestimation of \ce{Na^+} counterions and
 imperfect structures of the lipid headgroup (Fig.~\ref{simVSexpNOions_POPS}).
-The POPS headgroup order parameters are also related to the changes of average orientation of P--N and
-C$_{\beta}$--C$_{\gamma}$ vectors in the PS headgroup, which are smaller and more systematic
-in ECC-lipids than in Lipid7/Dang simulations (Fig.~\ref{fig:delta_ordPar_CaCl_PCPS}).
-Upon addition of 620~mM CaCl$_2$ to POPC:POPS (5:1) mixture,
-the average orientation of P--N vectors in both POPC and POPS headgroups tilts more perpendicular to the membrane surface
-by 11$^\circ$ and  3$^\circ$, respectively, in ECC-lipids simulations (Fig.~\ref{fig:delta_ordPar_CaCl_PCPS}),
-suggesting that the PS headgroup orientation is less sensitive to the bound calcium than PC.
-On the other hand, the average orientation of the C$_{\beta}$--C$_{\gamma}$ vector in PS headgroup
-tilts to the opposite direction by $11^\circ$ in the same system.
 
 Recent analyzes of interaction sites between calcium and PS lipids combining
-MD simulations with various experimental techniques have been 
-controversial because the results strongly depend on force fields parameters \cite{melcrova16,valentine18,hallock18}.
-Here, we analyze the calcium binding details from ECC-lipids simulation of POPC:POPS (5:1) mixture with 409 mM CaCl$_2$,
-because it surpasses the quality of other force fields in direct comparison with experimental order parameter data.
+MD simulations with various experimental techniques have been controversial 
+because the results strongly depend on force fields parameters \cite{melcrova16,valentine18,hallock18, NMRlipidsIV}.
+Here, we analyze the calcium binding details of POPC:POPS (5:1) mixture with 409 mM CaCl$_2$ from ECC-lipids simulations,
+which surpass the quality of other force fields in direct comparison with experimental order parameters.
 In the ECC-lipid simulation, calcium ions binds approximately twice more likely 
 to the carboxylate than to the phosphate moiety of POPS headgroup,
-while binding to acyl chain carbonyls is almost negligible (Fig.~\ref{fig:cacl_complexes} and table~\ref{tab:binding}).
+while binding only to acyl chain carbonyls is almost negligible (Fig.~\ref{fig:cacl_complexes} and Table~\ref{tab:binding}).
 The result is consistent with CHARMM36 simulations without the NBfix correction \cite{hallock18},
-but CHARMM36 simulations with the NBfix correction \cite{kim16} predict almost exclusive binding on carboxylate group \cite{valentine18}
-and Berger simulations signifincant binding affinity also on acyl chain carbonyls \cite{melcrova16}.
+but CHARMM36 simulations with the NBfix correction \cite{kim16} predict almost exclusive binding to carboxylate group \cite{valentine18}
+and Berger simulations show signifincant binding affinity also to acyl chain carbonyls \cite{melcrova16}.
 On the other hand, calcium ions bind too strongly on bilayers simulated using CHARMM36 without the NBfix correction
 or Berger models, and too weakly on CHARMM36 bilayers with the NBfix correction \cite{catte16,NMRlipidsIV}.
 Furthermore, in CHARMM36 simulations without the NBfix,
 calcium ions coordinate with even four distinct PS lipids \cite{hallock18}, while coordination with more than two PS lipids
-was very rare in our ECC-lipids simulations (Fig.~\ref{fig:cacl_complexes}).
-%Furthermore, the POPS:POPC:Ca$^{2+}$ (7:3:7) mixture with relatively high
-%PS lipid fraction and calcium concentration was used in the previous work \cite{hallock18},
-%which may lead to the complexation of \ce{Ca^{2+}} cations and PS lipids that is
-%not observed with lower PS content used in ECC-lipids simulations in this work \cite{hauser77,kurland79,hauser85,feigenson86,mattai89,roux90,roux91}.
-%While POPC interacts with the calcium cations almost entirely through its phosphate group 
-%in both neutral \cite{melcr18} and negatively charged membranes, 
-%the inteaction with POPS lipids happens more through the \ce{COO^-} group than through the \ce{PO4} group. 
-%Interactions of \ce{Ca^{2+}} with carbonyl groups are also present for both POPC and POPS,
-%however, they are always accompanied by interactions with phosphate groups. 
-
-%Significant coordination of calcium with carbonyl groups of PS and PC lipids observed in previous
-%simulations with the Berger force field \cite{melcrova16} %\cite{berger97,mukhopadhyay04}
-%was not observed in ECC-lipids simulations in here nor in the previous work with pure POPC \cite{melcr18}.
-%Overestimated coordination of cations with carbonyl groups is a potential source for
-%the overestimated cation binding in Berger force field \cite{catte16,NMRlipidsIV}. 
-%In CHARMM36 simulations with the NBfix, calcium mainly interacted with only
-%carboxylate of PS lipids  \cite{valentine18}, which is a potential source for the
-%underestimated calcium binding affinity to lipid bilayer with this force field \cite{NMRlipidsIV}. 
-
-%on average 41\% of the total population of bound calcium cations is in contact with PS lipids
-%with 8\% bound exclusively only to them even though the negatively charged membrane contains only 17\% of POPS (Fig.~\ref{fig:cacl_complexes}).
-%%Therefore, calcium ions bind more likely to negatively charged PS lipids than neutral PC lipid in a mixed bilayer, as expected.
-%	For comparison, in a pure POPC bilayer with 350 mM CaCl$_2$, 
-%	67\% of bound \ce{Ca^{2+}} is exclusively in contact with \ce{PO_4} group. \cite{melcr18} 
-
-
-%This can explain the diminished flexibility of the PS head group 
-%from simultaneous binding of \ce{Ca^{2+}} to the \ce{COO^-} group in PS and a phosphate group in PC 
-%as the most probable configuration (Fig.~\ref{fig:cacl_complexes}). 
-
-%In contrast, the combination of NMR experiments 
-%and MD simulations with the same model, CHARMM36, but without the correction for calcium binding
-%also reveal long-lived interactions of \ce{Ca^{2+}} with \ce{PO4} groups. \cite{hallock18}
-%Although the ratios of the life times of coordination follow the same trends as in our work,
-%the lengths of simulation trajectories are insufficient 
-%to yield converged results in this aspect (see SI and Refs.~\cite{catte16, melcr18, NMRlipidsIV}). 
+is very rare in our ECC-lipids simulations (Fig.~\ref{fig:cacl_complexes}).
+
+The improved accuracy in ECC-lipids simulations motivates also the more detailed analysis of
+POPS headgroup response to the bound calcium ions, which is potentially important in calcium regulated
+lipid-protein interactions \cite{leventis10}.
+Upon addition of 620~mM CaCl$_2$ to POPC:POPS (5:1) mixture,
+the average orientation of P--N vectors in both POPC and POPS headgroups tilts more perpendicular to the membrane surface
+by 11$^\circ$ and  3$^\circ$, respectively, in ECC-lipids simulations (Fig.~\ref{fig:delta_ordPar_CaCl_PCPS}),
+suggesting that the PS headgroup orientation is less sensitive to the bound calcium than PC.
+On the other hand, the average orientation of the C$_{\beta}$--C$_{\gamma}$ vector in PS headgroup
+tilts to the opposite direction by $11^\circ$ in the same system, probably
+due to the attraction between \ce{COO^-} groups and cations adsorbed at the phosphate region.
+
+
 
 \section{Conclusions} 
 We have applied ECC to implicitly include electronic polarization to the Amber Lipid17 force field
@@ -975,46 +793,39 @@ \section{Conclusions}
 Nevertheless, ECC-lipid parameters describe cation (Na$^+$ and Ca$^{2+}$) binding affinities
 and their interactions with PS headgroups better than other available lipid force fields,
 when validated using the headgroup order parameters and ``electrometer concept''~\cite{NMRlipidsIV}.
-There is, however, room for improvement in capturing the sensitive headgroup responses to the
+There is, however, still room for improvement in capturing the sensitive headgroup responses to 
 small concentrations of CaCl$_2$.
 
 In our ECC-lipids simulation, Ca$^{2+}$ ions bind twice more likely to carboxylate groups
-of PS headgroups than to phosphate groups, while binding to carbonyls is almost negligible.
-Binding of Ca$^{2+}$ ions to more than two POPS lipids simultaneously is very rare in ECC-lipids simulations.
-Because ECC-lipids parameters give the best results in direct comparison with NMR order parameters, 
-we believe that our results help in resoving controversial interpretations of more indirect experiments
-using different force fields~\cite{melcrova16,valentine18,hallock18}.
-%measured and simulation data, which enables more unambiguous evaluation of the force field quality \cite{catte16,ollila16}
-%than more indirect comparison in previous studies using 2D infrared spectroscopy \cite{valentine18}, NMR chemical shifts and
-%rotational-echo double-resonance (REDOR) experiments \cite{hallock18} or fluorescent and vibrational sum frequency spectroscopy \cite{melcrova16}.
-%Because the ECC-lipids model gives the best agreement with the experimental headgroup order parameters
-%with various ion conctenrations among the available models, we believe that it also gives the currently best available
-%interpretation of the experimental data. 
-Furthermore, our results pave the way for more realistic MD simulations of anionic biological membranes,
-and demonstrate the usefulness of ECC also for charged lipids.
-\todo{Maybe Pavel could extend this by mentioning something that this is yet another case where ECC works and/or
-  mentioning some concrete biological examples where anionic membrane/calcium interactions are important?}
-
-%Therefore, further force field optimization is required for even more accurate MD simulations of cations
-%in the vicinity of negatively charged lipid bilayers.
-
-
-
-\listoftodos
-
+of PS headgroups than to phosphate groups, while binding only to carbonyls is negligible.
+However, calcium can bind also to carbonyls when simultaneously bound also to carboxylate (Fig. \ref{fig:strcutures_SI}) or phosphate group.
+Binding of Ca$^{2+}$ ions to more than two POPS lipids simultaneously is very rare in \mbox{ECC-lipids} simulations.
+Because \mbox{ECC-lipids} parameters give the best results in direct comparison with NMR order parameters, 
+we believe that our results help in resolving controversial interpretations of more indirect experiments
+using different force fields~\cite{melcrova16,valentine18,hallock18}
+and demonstrate the usefulness of ECC also for membranes with charged lipids.
+Furthermore, the present simulations pave the way
+for more realistic MD simulations of biomolecular systems with anionic membranes
+allowing to elucidate signaling processes involving PS and \ce{Ca^{2+}}. 
+
+
+The general philosophy behind our approach is to build upon existing non-polarizable force fields making the minimum of necessary changes by scaling only groups bearing a sizeable (partial) charge, followed by slight readjustments of van der Waals radii and possibly also other parameters such as those concerning dihedral angle terms.
+The present work thus represents another piece in the mosaic that leads to development of an improved empirical force field for biomolecular simulations involving aqueous salt solutions, proteins, peptides, lipid membranes, and/or nucleic acids, which include electronic polarization effects in a mean field way via charge scaling without extra computational costs compared to standard non-polarizable simulations. 
+We believe that such ECC force fields will be useful in modeling complex biomembranes when simulations with
+explicitly polarizable force fields for biomolecules \cite{amoeba13,li17,chu18} are not practical.
 
 % If you have acknowledgments, this puts in the proper section head. 
 \begin{acknowledgement} 
 % Put your acknowledgments here. 
-P.J. acknowledges support from the Czech Science Foundation (grant no. 16-01074S)  
-and from the Academy of Finland via the FiDiPro award. 
+P.J. acknowledges support from the Czech Science Foundation via an EXPRO grant no. 19-26854X. 
 Computational resources were supplied by the Ministry of Education, Youth and Sports 
 of the Czech Republic under the Projects CESNET (Project No. LM2015042) and CERIT-Scientific 
 Cloud (Project No. LM2015085) provided within the program Projects of Large Research, 
 Development and Innovations Infrastructures. 
-O.H.S.O. acknowledges financial support from 
-Integrated Structural Biology Research Infrastructure of 
-Helsinki Institute of Life Science (Instruct-HiLIFE). 
+O.H.S.O. acknowledges financial support from Academy of Finland (315596),
+Integrated Structural Biology Research Infrastructure of
+Helsinki Institute of Life Science (Instruct-HiLIFE), and
+CSC-IT center for science for computational resources.
 \end{acknowledgement} 
  
 \begin{suppinfo} 
@@ -1024,10 +835,12 @@ \section{Conclusions}
 %Supporting Information as well as how to prepare this material for 
 %publications, refer to the journal's Instructions for Authors. 
  
-%The following files are available free of charge. 
-%\begin{itemize} 
-%  \item Filename: brief description 
-%\end{itemize} 
+The following files are available free of charge. 
+\begin{itemize} 
+\item SI.pdf: Measured 1D and 2D NMR spectra, additional details and results from simulations
+  about monovalent ion binding, configurations and populations of bound calcium to POPS lipids, and
+  residence times of bound calcium.
+\end{itemize} 
  
 \end{suppinfo} 
  
diff --git a/Manuscript/manuscriptSUPPL.pdf b/Manuscript/manuscriptSUPPL.pdf
new file mode 100644
index 0000000..2ca1691
Binary files /dev/null and b/Manuscript/manuscriptSUPPL.pdf differ
diff --git a/Manuscript/manuscriptSUPPL.tex b/Manuscript/manuscriptSUPPL.tex
index c277a0b..5250818 100644
--- a/Manuscript/manuscriptSUPPL.tex
+++ b/Manuscript/manuscriptSUPPL.tex
@@ -3,7 +3,7 @@
 %% The document class accepts keyval options, which should include 
 %% the target journal and optionally the manuscript type. 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-\documentclass[journal=jpcbfk,manuscript=article]{achemso} 
+\documentclass[journal=jctcce,manuscript=article]{achemso} 
  
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %% Place any additional packages needed here.  Only include packages 
@@ -78,7 +78,7 @@
 \newlength{\figwidthsmall}
 \setlength{\figwidthsmall}{6 cm} 
 \newlength{\figwidthfull}
-\setlength{\figwidthfull}{14 cm} 
+\setlength{\figwidthfull}{16 cm} 
 \newlength{\figheightsmall}
 \setlength{\figheightsmall}{6 cm} 
 \newlength{\figheight}
@@ -108,25 +108,24 @@
  
 \author{Josef Melcr} 
 \email{melcr@marge.uochb.cas.cz} 
-%%\homepage[]{https://jmelcr.github.io/}
-\affiliation{Institute of Organic Chemistry and Biochemistry, 
-Academy of Sciences of the Czech Republic,  
-Prague 6, Czech Republic} 
+\affiliation[Czech Academy of Sciences]{Institute of Organic Chemistry and Biochemistry of the 
+Czech Academy of Sciences, Flemingovo n\'{a}m. 542/2, CZ-16610 Prague 6, Czech Republic}
+\alsoaffiliation{Groningen Biomolecular Sciences and Biotechnology Institute 
+and The Zernike Institute for Advanced Materials, 
+University of Groningen, 9747 AG Groningen, The Netherlands}
+
+\author{Tiago M. Ferreira}
+\affiliation{NMR group - Institut for Physics, Martin-Luther University Halle-Wittenberg} 
 \author{Pavel Jungwirth} 
 %%\homepage[]{http://jungwirth.uochb.cas.cz/}
 \affiliation{Institute of Organic Chemistry and Biochemistry, 
-Academy of Sciences of the Czech Republic,  
+Czech Academy of Sciences,  
 Prague 6, Czech Republic} 
-\alsoaffiliation{Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 
-Tampere, Finland} 
-%SAMULI: We need to put tiago because the experimental acyl chain order parameters
-\author{Tiago Ferreira}
-\affiliation{Halle} 
 \author{O. H. Samuli Ollila} 
 \email{samuli.ollila@helsinki.fi} 
 %%\homepage[]{Your web page} 
 \affiliation{Institute of Organic Chemistry and Biochemistry, 
-Academy of Sciences of the Czech Republic,  
+Czech Academy of Sciences,  
 Prague 6, Czech Republic} 
 \alsoaffiliation{Institute of Biotechnology, University of Helsinki} 
  
@@ -160,28 +159,22 @@
 %% a running title from the author: this should be supplied as an 
 %% optional argument to \title. 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-%\title[] 
-%  {Accurate interactions of cations with 
-%   neutral and negatively charged membranes 
-%   via combination of experiments and molecular simulation}
-
-%%SAMULI: new suggestion for the preliminary title
 \title[] 
-  { SUPPLEMENTARY INFORMATION: Improved Cation Binding to Lipid Bilayer with Negatively Charged POPS by Effective Inclusion of Electronic Polarization}
-%    Detailed structure of negatively charged membranes 
-%    of phosphatidylserine and phosphatidylcholine 
-%    at concentrations of calcium, sodium and potassium salts
-%    from molecular dynamics simulations with electronic polarization }
+      { SUPPLEMENTARY INFORMATION: 
+        Improved Cation Binding to Lipid Bilayer with
+        Negatively Charged POPS by Effective
+        Inclusion of Electronic Polarization
+      }
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %% Some journals require a list of abbreviations or keywords to be 
 %% supplied. These should be set up here, and will be printed after 
 %% the title and author information, if needed. 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-\abbreviations{IR,NMR,UV,MD,ECC,PC,PS,POPS,POPS} 
-\keywords{MD simulation, molecular modeling, 
-          polarizability, polarization,
-          phospholipids, phosphatidylserine} 
+%\abbreviations{IR,NMR,UV,MD,ECC,PC,PS,POPS,POPS} 
+%\keywords{MD simulation, molecular modeling, 
+%          polarizability, polarization,
+%          phospholipids, phosphatidylserine} 
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %% The manuscript does not need to include \maketitle, which is 
@@ -195,14 +188,39 @@
 
 
 \begin{document} 
- 
+
+\clearpage
+\section{Simulation details}
+\begin{table}[!h]
+  \caption{Simulation parameters}
+  \label{tbl:mdpar}
+  \begin{tabular}{ll}
+    simulation property & parameter   \\
+    \hline
+    time-step           & 2~fs         \\
+    equilibration time  & 50~ns  \\
+    total simulation time     & $\geq 1 \mu$s  \\
+    temperature         & 298~K       \\
+    thermostat          & v-rescale  \cite{bussi07}   \\
+    barostat            & Parrinello-Rahman, semi-isotropic \cite{parrinello81} \\
+    long-range electrostatics & PME  \cite{darden93}  \\
+    cut-off scheme      & Verlet \cite{Pall13}      \\
+    Coulomb and VdW cut-off & 1.0~nm \\
+    constraints         & LINCS, only hydrogen atoms \cite{hess97} \\
+    constraints for water & SETTLE  \cite{miyamoto92} \\
+    \hline
+  \end{tabular}
+\end{table}
+
+\clearpage
 \section{NMR experiments}
 
 \begin{figure}[!h] 
   \centering 
   \includegraphics[width=\textwidth]{../Fig/POPSINEPT.pdf}
   \caption{\label{INEPT}
-    Refocused-INEPT $^{13}$C spectrum of POPS multilamellar vesicles.
+    Refocused-INEPT $^{13}$C spectrum of multilamellar POPS vesicles at 298 K
+    with peak assignments for non--crowded spectral region ({\it sn}-1 chain in parenthesis).
   }
 \end{figure}
 
@@ -210,7 +228,8 @@ \section{NMR experiments}
   \centering 
   \includegraphics[width=\textwidth]{../Fig/crowded_region.pdf}
   \caption{\label{R-PDLF}
-    2D-NMR R-PDLF spectra from the acyl chain region of POPS lipid bilayer.
+    2D-NMR R-PDLF spectra from the crowded spectral region of multilamellar POPS vesicles with the peak
+    assignment. Apostrophes refer to the palmitoyl ({\it sn}-1) chain.
   }
 \end{figure}
 
@@ -218,7 +237,8 @@ \section{NMR experiments}
   \centering 
   \includegraphics[width=\textwidth]{../Fig/slices_used.eps}
   \caption{\label{R-PDLFslices}
-    Dipolar slices from the R-PDLF spectra used to determine the acyl chain order parameters of POPS.
+    Dipolar slices from the R-PDLF spectra of multilamellar POPS vesicles used to determine the acyl chain order parameters.
+    Numbers of on top of figures refer to the chemical shift (left) and order parameter value (right).
   }
 \end{figure} 
 
@@ -244,29 +264,21 @@ \section{NMR experiments}
 \section{Interactions of POPS with \ce{K+} and \ce{Na+} counterions and POPC}
 
 % SAMULI: I have moded the density profile figure in the main text
-\begin{figure}[hbp!] 
+\begin{figure}[!h] 
   \centering 
-%  \includegraphics[height=\figheightsmall]{../img/ecc_pops/density_profiles_na-k-counterions_wat_phos_compar_purePOPS_ecclipids-lipid17.pdf}
-  \includegraphics[height=\figheightsmall]{../Fig/order_parameters_changes_A-B_PC-PS_mix_POPS_nacl.pdf} 
-  \includegraphics[height=\figheightsmall]{../Fig/order_parameters_changes_A-B_PC-PS_mix_POPS_kcl.pdf} 
-%  \caption{\label{fig:POPS-counterions-dens}
-%    \textbf{Left panel:} Number density profiles of \ce{K^{+}} and \ce{Na^{+}} counterions along the membrane normal axis
-%    in ECC-lipids (solid lines) and Lipid17/Dang (dashed lines) simulations of pure POPS bilayers.  
-%    The density profiles of phosphate groups and water are divided by 4 and 100, respectively.  
-%}
+  \includegraphics[width=\figwidthfull]{../img/deltaOP_mix_PC-PS_SupplInf-POPS-OP.pdf} 
   \caption{\label{fig:delta_ordPar_NaCl_PC-PS_mix_PS} 
-    %\textbf{Right panels:}
-    The POPS head group order parameters, the P--N (circles) and C$_\beta$--C$_\gamma$ vector angles (stars)
+    \textbf{(A)} Number density profiles of \ce{K^{+}} and \ce{Na^{+}} counterions along the membrane normal axis
+    in ECC-lipids (solid lines) and Lipid17/Dang (dashed lines) simulations of POPC:POPS (5:1) bilayers.  
+    The density profiles of phosphate groups and water are divided by 4 and 100, respectively.  
+    \textbf{(B, C)} The POPS head group order parameters, the P--N (circles) and C$_\beta$--C$_\gamma$ vector angles (stars) 
     with respect to the membrane normal as a function of POPC content in a bilayer
-    from ECC-lipids and Lipid17/Dang simulations with \ce{Na^+} (left) and \ce{K^+} (right) counterions.
-    Experimental order parameter values and signs for pure POPS are from Ref. \citenum{NMRlipidsIV} and values
-    for POPC:POPS (5:1) mixture from Ref. \citenum{roux90} 
-    (only \ce{Na^+} counterions, but shown with dashed lines also in the right hand side plots for \ce{K+}).
-    % No translation in y-axis done in this plot:
-    %The underestimated response of ECC-lipids with \ce{Na^+} counterions 
-    %is likely due to a still slightly overestimated binding affinity of \ce{Na^+} to the phospholipids,
-    %which is corroborated by the series with \ce{K^+} counterions (lower affinity than \ce{Na^+}),
-    %where the response is closer to the experiment, which uses only \ce{Na^+} counterions. 
+    from ECC-lipids and Lipid17/Dang simulations with \ce{Na^+} (C) and \ce{K^+} (B) counterions.
+    Experimental order parameter values are from Ref. \citenum{scherer87}
+    and the signs from Ref.~\citenum{ferreira16} 
+    (only \ce{Na^+} counterions, but shown also in the left plots (B) for \ce{K+} with dashed lines).
+    Error bars are not visible for most of the simulation points because they are smaller than the point size.
+    Chemical structure and labelling of carbon segments of POPC is shown in Fig.~\ref{fig:delta_ordPar_monoval_PCPS} in the main text. 
   }
 \end{figure} 
 
@@ -289,6 +301,24 @@ \section{Density profiles of additional monovalent cations in POPC:POPS (5:1) mi
 \end{figure} 
 
 
+\pagebreak
+
+
+
+
+\section{Representative example configurations of \ce{Ca^{2+}} coordinated complexes with POPS phospholipids}
+
+\begin{figure}[!h] 
+  \centering 
+  \includegraphics[width=\figwidthfull]{../img/populations_stoichiometry_structures_SI.pdf}
+  \caption{\label{fig:strcutures_SI} 
+    Representative example configurations of \ce{Ca^{2+}} coordinated complexes 
+    of only one POPS (A), one POPS with one POPC (B) or two POPS lipids (C). 
+    Probabilities of different calcium-phospholipid complexes are shown in Fig.~\ref{fig:cacl_complexes} in the main text. 
+  }
+\end{figure} 
+
+
 \pagebreak
 \section{Populations of bound \ce{Ca^{2+}} cations to the PC:PS (5:1) bilayer}
 
@@ -325,24 +355,22 @@ \section{Populations of bound \ce{Ca^{2+}} cations to the PC:PS (5:1) bilayer}
       PC and COO$^-$ in PS   &   17   &        \\
       PC and carbonyls in PS &   <1   &        \\
   \end{tabular} \\
-  %\todo{I have commented out the surface excess values (available in text) and concentrations (now in caption) from the table.} \\
-  %\todo{I do not understand the numbers for different moieties. Are these probabilities that the calcium binds only to these moieties and
-  %  nothing else? In total, 41 \% binds to PS lipids, but only 2 \% and 4 \% to phosphates and COO$^-$, respectively? Where do the rest bind?
-  %  I think that we should show the total probabilities to bind to different moieties.}
 \end{table} 
 
 
 \pagebreak
 \section{Residence times of cations}
 
-In ECC-lipid simulations, 90\% of the calcium residence times are shorter than $60\,\mathrm{ns}$ for pure POPC bilayer
-and shorter than $200\,\mathrm{ns}$ for POPC:POPS (5:1) mixture, while the
-longest observed residence times are $141\,\mathrm{ns}$ and $485\,\mathrm{ns}$, respectively (Fig.~\ref{fig:hist_residence_times}).
-The significantly shorter residence times in ECC-lipid simulations than in simulations 
-with other force fields~\cite{javanainen17, catte16} suggests that 1~$\mu$s simulations in this work
-are sufficiently long to equlibrate the ion concentration on lipid bilayer interface.
-Interestingly, the calcium residence times are 3-4 times longer in POPC:POPS (5:1) mixture than in
-pure POPC.
+% Already in the main text
+%
+%In ECC-lipid simulations, 90\% of the calcium residence times are shorter than $60\,\mathrm{ns}$ for pure POPC bilayer
+%and shorter than $200\,\mathrm{ns}$ for POPC:POPS (5:1) mixture, while the
+%longest observed residence times are $141\,\mathrm{ns}$ and $485\,\mathrm{ns}$, respectively (Fig.~\ref{fig:hist_residence_times}).
+%The significantly shorter residence times in ECC-lipid simulations than in simulations 
+%with other force fields~\cite{javanainen17, catte16} suggests that 1~$\mu$s simulations in this work
+%are sufficiently long to equlibrate the ion concentration on lipid bilayer interface.
+%Interestingly, the calcium residence times are 3-4 times longer in POPC:POPS (5:1) mixture than in
+%pure POPC.
 
 %Both estimates of the residence times come from simulations with comparable concentrations of around $250\mathrm{mM}$;
 %the simulation with the neutral membrane has a bulk concentration of calcium $C_{ion} = 280\mathrm{mM}$, 
diff --git a/Manuscript/refs.bib b/Manuscript/refs.bib
index 254a3fc..ead85d8 100644
--- a/Manuscript/refs.bib
+++ b/Manuscript/refs.bib
@@ -11,6 +11,112 @@
 %
 %  ===========================================================================
 
+@article{vazdar13,
+author = {Vazdar, Mario and Jungwirth, Pavel and Mason, Philip E.},
+title = {Aqueous Guanidinium–Carbonate Interactions by Molecular Dynamics and Neutron Scattering: Relevance to Ion–Protein Interactions},
+journal = {J. Phys. Chem. B},
+volume = {117},
+number = {6},
+pages = {1844-1848},
+year = {2013},
+}
+
+@article{bruce18,
+author = {Bruce,Ellen E.  and van der Vegt,Nico F. A. },
+title = {Does an electronic continuum correction improve effective short-range ion-ion interactions in aqueous solution?},
+journal = {J. Chem. Phys.},
+volume = {148},
+number = {22},
+pages = {222816},
+year = {2018},
+}
+
+
+@article{kroutil17,
+author="Kroutil, Ond{\v{r}}ej
+and P{\v{r}}edota, Milan
+and Kabel{\'a}{\v{c}}, Martin",
+title="Force field parametrization of hydrogenoxalate and oxalate anions with scaled charges",
+journal="J. Mol. Model.",
+year="2017",
+month="Oct",
+day="28",
+volume="23",
+number="11",
+pages="327",
+}
+
+
+@article{xie16,
+author = {Xie, Wen Jun and Zhang, Zhen and Gao, Yi Qin},
+title = {Ion Pairing in Alkali Nitrate Electrolyte Solutions},
+journal = {J. Phys. Chem. B},
+volume = {120},
+number = {9},
+pages = {2343-2351},
+year = {2016},
+}
+
+
+
+@article{kohagen14b,
+author = {Kohagen, Miriam and Lepšík, Martin and Jungwirth, Pavel},
+title = {Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization},
+journal = {J. Phys. Chem. Lett.},
+volume = {5},
+number = {22},
+pages = {3964-3969},
+year = {2014},
+}
+
+
+
+@article{pluharova13,
+author = {Pluhařová, Eva and Mason, Philip E. and Jungwirth, Pavel},
+title = {Ion Pairing in Aqueous Lithium Salt Solutions with Monovalent and Divalent Counter-Anions},
+journal = {J. Phys. Chem. A},
+volume = {117},
+number = {46},
+pages = {11766-11773},
+year = {2013},
+}
+
+
+
+@article{li17,
+author = {Li, Hui and Chowdhary, Janamejaya and Huang, Lei and He, Xibing and MacKerell, Alexander D. and Roux, Benoît},
+title = {Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids},
+journal = {J. Chem. Theory Comput.},
+volume = {13},
+number = {9},
+pages = {4535-4552},
+year = {2017},
+}
+
+@article{chu18,
+AUTHOR = {Chu, Huiying and Peng, Xiangda and Li, Yan and Zhang, Yuebin and Li, Guohui},
+TITLE = {A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids},
+JOURNAL = {Molecules},
+VOLUME = {23},
+YEAR = {2018},
+NUMBER = {1},
+ARTICLE-NUMBER = {77},
+}
+
+
+
+
+@article{han2018graph,
+  Title={Graph--Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions},
+  author={Han, Kyungreem and Venable, Richard M and Bryant, Anne-Marie and Legacy, Christopher J and Shen, Rong and Li, Hui and Roux, Beno{\^\i}t and Gericke, Arne and Pastor, Richard W},
+  journal={J. Phys. Chem. B},
+  volume={122},
+  number={4},
+  pages={1484--1494},
+  year={2018},
+  publisher={ACS Publications}
+}
+
 @article{yeung08,
 	author = {Yeung, Tony and Gilbert, Gary E. and Shi, Jialan and Silvius, John and Kapus, Andras and Grinstein, Sergio},
 	title = {Membrane Phosphatidylserine Regulates Surface Charge and Protein Localization},
@@ -25,7 +131,7 @@ @article{yeung08
 
 @article{gorbenko06,
 title = "The role of lipid–protein interactions in amyloid-type protein fibril formation",
-journal = "Chemistry and Physics of Lipids",
+journal = "Chem. Phys. Lipids",
 volume = "141",
 number = "1",
 pages = "72 - 82",
@@ -46,7 +152,7 @@ @article{zhao04
 
 @article{li14,
 title = "Ionic protein–lipid interaction at the plasma membrane: what can the charge do?",
-journal = "Trends in Biochemical Sciences",
+journal = "Trends Biochem. Sci.",
 volume = "39",
 number = "3",
 pages = "130 - 140",
@@ -57,7 +163,7 @@ @article{li14
 
 @article{kim16,
 title = "Bilayer Properties of Lipid A from Various Gram-Negative Bacteria",
-journal = "Biophysical Journal",
+journal = "Biophys. J.",
 volume = "111",
 number = "8",
 pages = "1750 - 1760",
@@ -71,7 +177,7 @@ @article{kim16
 @article{agrawal11,
 author = {Michaud-Agrawal, Naveen and Denning, Elizabeth J. and Woolf, Thomas B. and Beckstein, Oliver},
 title = {MDAnalysis: A toolkit for the analysis of molecular dynamics simulations},
-journal = {Journal of Computational Chemistry},
+journal = {J. Comput. Chem.},
 volume = {32},
 number = {10},
 year = {2011},
@@ -91,15 +197,35 @@ @InProceedings{gowers16
   editor    = { {S}ebastian {B}enthall and {S}cott {R}ostrup }
 }
 
+%% REFERENCE TO BE UPDATED
+%  according to the current status at submittion
+%
 @misc{MATCHgit,
-  author       = {ohsOllila and et al.},
+author ="
+Amelie Bacle and
+Pavel Buslaev and
+Lukasz Cwiklik and
+Fernando Favela and
+Tiago Ferreira and
+Patrick Fuchs and
+Ivan Gushchin and
+Matti Javanainen and
+Batuhan Kav and
+Jesper Madsen and
+Josef Melcr and
+Markus Miettinen and
+Ricky Nencini and
+Samuli Ollila and
+Chris Papadopoulos and
+Thomas Piggot
+",
   title       = {MATCH GitHub repository},
   url         = {https://github.com/NMRLipids/MATCH}
 }
 
 @article{fung00,
 title = "An Improved Broadband Decoupling Sequence for Liquid Crystals and Solids",
-journal = "Journal of Magnetic Resonance",
+journal = "J. Magn. Res.",
 volume = "142",
 number = "1",
 pages = "97 - 101",
@@ -113,7 +239,7 @@ @article{fung00
 @article{morris79,
 author = {Morris, Gareth A. and Freeman, Ray},
 title = {Enhancement of nuclear magnetic resonance signals by polarization transfer},
-journal = {Journal of the American Chemical Society},
+journal = {J. Am. Chem. Soc.},
 volume = {101},
 number = {3},
 pages = {760-762},
@@ -122,7 +248,7 @@ @article{morris79
 
 @article{burum80,
 title = "Net polarization transfer via a J-ordered state for signal enhancement of low-sensitivity nuclei",
-journal = "Journal of Magnetic Resonance (1969)",
+journal = "J. Magn. Res.",
 volume = "39",
 number = "1",
 pages = "163 - 168",
@@ -143,18 +269,22 @@ @article{lemmon08
 }
 
 
-@misc{NMRlipidsIV,
-  author       = {Pavel Buslaev and Fernando Favela and Tiago M. Ferreira and Ivan Gushchin and Matti Javanainen and Batuhan Kav and Jesper J. Madsen and Markus Miettinen and Josef Melcr and Ricky Nencini and O. H. Samuli Ollila and Thomas Piggot},
-  title        = {{NMRlipids IV: Headgroup and glycerol backbone structures, and cation binding in bilayers with PS
-lipids}},
-  year         = 2018,
-  url          = {https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/Manuscript/manuscriptPS.pdf}
+@article{NMRlipidsIV,
+author = {Antila, Hanne S. and Buslaev, Pavel and Favela-Rosales, Fernando and {Mendes Ferreira}, Tiago and Gushchin, Ivan and Javanainen, Matti and Kav, Batuhan and Madsen, Jesper J. and Melcr, Josef and Miettinen, Markus Sakari and M{\"{a}}{\"{a}}tt{\"{a}}, Jukka and Nencini, Ricky and Ollila, O. H. Samuli and Piggot, Thomas J},
+doi = {10.1021/acs.jpcb.9b06091},
+journal = {J. Phys. Chem. B},
+pages = {9066-9079},
+title = {{Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers}},
+year = {2019},
+volume ={123}
 }
 
+
+
 @article{leventis10,
 author = {Peter A. Leventis and Sergio Grinstein},
 title = {The Distribution and Function of Phosphatidylserine in Cellular Membranes},
-journal = {Annual Review of Biophysics},
+journal = {Annu. Rev. Biophys.},
 volume = {39},
 number = {1},
 pages = {407-427},
@@ -163,7 +293,7 @@ @article{leventis10
 
 @article{hauser77,
 title = "Crystalline anhydrous Ca-phosphatidylserine bilayers",
-journal = "Biochemical and Biophysical Research Communications",
+journal = "Biochem. Biophys. Res. Commun.",
 volume = "76",
 number = "2",
 pages = "267 - 274",
@@ -175,8 +305,8 @@ @article{hauser77
 }
 
 @article{kurland79,
-title = "Binding of Ca2+ and Mg2+ to phosphatidylserine vesicles: Different effects on P-31 NMR shifts and relaxation times",
-journal = "Biochemical and Biophysical Research Communications",
+title = "Binding of Ca$^{2+}$ and Mg$^{2+}$ to phosphatidylserine vesicles: Different effects on P-31 NMR shifts and relaxation times",
+journal = "Biochem. Biophys. Res. Commun.",
 volume = "88",
 number = "3",
 pages = "927 - 932",
@@ -189,7 +319,7 @@ @article{kurland79
 
 @article{hauser85,
 title = "Comparative structural aspects of cation binding to phosphatidylserine bilayers",
-journal = "Biochimica et Biophysica Acta (BBA) - Biomembranes",
+journal = "Biochim. Biophys. Acta",
 volume = "813",
 number = "2",
 pages = "343 - 346",
@@ -253,11 +383,10 @@ @article{dluhy83
 
 @article{sinn06,
 title = "Binding of calcium to phosphatidylcholine–phosphatidylserine membranes",
-journal = "Colloids and Surfaces A: Physicochemical and Engineering Aspects",
+journal = "Colloids Surf. A",
 volume = "282-283",
 pages = "410 - 419",
 year = "2006",
-note = "A Collection of Papers in Honor of Professor Ivan B. Ivanov (Laboratory of Chemical Physics and Engineering, University of Sofia) Celebrating his Contributions to Colloid and Surface Science on the Occasion of his 70th Birthday",
 author = "Cornelia G. Sinn and Markus Antonietti and Rumiana Dimova",
 keywords = "Vesicles, Model membranes, Calcium binding, Adsorption, Isothermal titration calorimetry, Giant unilamellar vesicles, Ion selective electrode"
 }
@@ -512,10 +641,35 @@ @article{papahadjopoulos90
 pages="157--179",
 }
 
-@misc{martinek17,
+
+@article{verma2018cell,
+  title={Cell-surface phosphatidylserine regulates osteoclast precursor fusion},
+  author={Verma, Santosh K and Leikina, Evgenia and Melikov, Kamran and Gebert, Claudia and Kram, Vardit and Young, Marian F and Uygur, Berna and Chernomordik, Leonid V},
+  journal={J. Biol. Chem.},
+  volume={293},
+  number={1},
+  pages={254--270},
+  year={2018},
+  publisher={ASBMB}
+}
+
+
+@article{wilschut1981calcium,
+  title={Calcium/magnesium specificity in membrane fusion: kinetics of aggregation and fusion of phosphatidylserine vesicles and the role of bilayer curvature},
+  author={Wilschut, Jan and Duezguenes, Nejat and Papahadjopoulos, Demetrios},
+  journal={Biochemistry},
+  volume={20},
+  number={11},
+  pages={3126--3133},
+  year={1981},
+  publisher={ACS Publications}
+}
+
+
+@article{martinek17,
   title={Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering},
   author={Mart{\'i}nek, Tom{\'a}{\v{s}} and Dubou{\'e}-Dijon, Elise and Timr, {\v{S}}t{\v{e}}p{\'a}n and Mason, Philip E and Baxov{\'a}, Katarina and Fischer, Henry E and Schmidt, Burkhard and Pluha{\v{r}}ov{\'a}, Eva and Jungwirth, Pavel},
-  journal={The Journal of chemical physics},
+  journal={J. Chem. Phys.},
   volume={148},
   number={22},
   pages={222813},
@@ -528,7 +682,7 @@ @article{duboue2018insulin
 author = {Dubou{\'{e}}-Dijon, Elise and Delcroix, Pauline and Martinez-Seara, Hector and Hlad{\'{i}}lkov{\'{a}}, Jana and Coufal, Pavel and Kř{\'{i}}{\v{z}}ek, Tom{\'{a}}{\v{s}} and Jungwirth, Pavel},
 doi = {10.1021/acs.jpcb.7b12097},
 issn = {1520-6106},
-journal = {The Journal of Physical Chemistry B},
+journal = {J. Phys. Chem. B},
 month = {may},
 number = {21},
 pages = {5640--5648},
@@ -540,21 +694,23 @@ @article{duboue2018insulin
 }
 
 @article{Mason2019,
-author = {Mason, PE and Jungwirth, P and Dubou{\'{e}}-Dijon, E},
+  title={Quantifying the strength of a salt bridge by neutron scattering and molecular dynamics},
+  author={Mason, Philip E and Jungwirth, Pavel and Dubou{\'e}-Dijon, Elise},
+  journal={J. Phys. Chem. Lett.},
+  year={2019},
+  publisher={ACS Publications},
 doi = {10.26434/CHEMRXIV.8025062},
-mendeley-groups = {MD simulations - technics},
-publisher = {ChemRxiv},
-title = {{Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics}},
-url = {https://europepmc.org/abstract/ppr/ppr76982},
-year = {2019}
+url = {https://europepmc.org/abstract/ppr/ppr76982}
 }
 
+
+
 @article{Duboue2018MgZn,
 abstract = {Magnesium and zinc dications possess the same charge and have an almost identical size, yet they behave very differently in aqueous solutions and play distinct biological roles. It is thus crucial to identify the origins of such different behaviors and to assess to what extent they can be captured by force-field molecular dynamics simulations. In this work, we combine neutron scattering experiments in a specific mixture of H2O and D2O (the so-called null water) with ab initio molecular dynamics simulations to probe the difference in the hydration structure and ion-pairing properties of chloride solutions of the two cations. The obtained data are used as a benchmark to develop a scaled-charge force field for Mg2+ that includes electronic polarization in a mean field way. We show that using this electronic continuum correction we can describe aqueous magnesium chloride solutions well. However, in aqueous zinc chloride specific interaction terms between the ions need to be introduced to capture ion pairing q...},
 author = {Dubou{\'{e}}-Dijon, Elise and Mason, Philip E. and Fischer, Henry E. and Jungwirth, Pavel},
 doi = {10.1021/acs.jpcb.7b09612},
 issn = {15205207},
-journal = {Journal of Physical Chemistry B},
+journal = {J. Phys. Chem. B},
 mendeley-groups = {MD simulations - technics},
 month = {apr},
 number = {13},
@@ -606,14 +762,14 @@ @misc{ecclipids_pcps_nacl_kcl_series
                    containing POPC and POPS (5:1) with ECC-lipids
                    force field, and Na+ (K+) counterions at various
                    additional concentrations of NaCl and KCl}},
-  month        = nov,
-  year         = 2018,
-  doi          = {10.5281/zenodo.1488110},
-  url          = {https://doi.org/10.5281/zenodo.1488110}
+  month        = July,
+  year         = 2019,
+  doi          = {10.5281/zenodo.3332778},
+  url          = {https://doi.org/10.5281/zenodo.3332778}
 }
 
 @misc{ecclipids_pcps_cacl2_series,
-  author       = {Melcr Josef},
+  author       = {Melcr, Josef},
   title        = {{Molecular dynamics simulations of lipid bilayers 
                    containing POPC and POPS (5:1) with ECC-lipids
                    force field, and Na+ (K+) counterions at various
@@ -776,7 +932,7 @@ @article{Seelig75
 
 @article{mukhopadhyay04,
 title = "Molecular Dynamics Simulation of a Palmitoyl-Oleoyl Phosphatidylserine Bilayer with Na+ Counterions and NaCl",
-journal = "Biophysical Journal",
+journal = "Biophys. J.",
 volume = "86",
 number = "3",
 pages = "1601 - 1609",
@@ -786,9 +942,9 @@ @article{mukhopadhyay04
 
 
 @Article{melcrova16,
-author ="Adéla Melcrov{\' a} and Šárka Pokorná and Saranya Pullanchery and Miriam Kohagen and Piotr Jurkiewicz and Martin Hof and Pavel Jungwirth and Paul S. Cremer and Lukasz Cwiklik",
+author ="Adéla Melcrov{\' a} and {\v{S}}árka Pokorná and Saranya Pullanchery and Miriam Kohagen and Piotr Jurkiewicz and Martin Hof and Pavel Jungwirth and Paul S. Cremer and Lukasz Cwiklik",
 title  ="The complex nature of calcium cation interactions with phospholipid bilayers",
-journal  ="Sci. Reports",
+journal  ="Sci. Rep.",
 year  ="2016",
 volume  ="6",
 pages  ="38035",
@@ -822,7 +978,7 @@ @article{hallock18
 
 @article{valentine18,
 title = "Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface",
-journal = "Biophysical Journal",
+journal = "Biophys. J.",
 volume = "115",
 number = "8",
 pages = "1541 - 1551",
@@ -1101,7 +1257,7 @@ @article{openmm7
 @article{amoeba10,
   title={Current status of the AMOEBA polarizable force field},
   author={Ponder, Jay W and Wu, Chuanjie and Ren, Pengyu and Pande, Vijay S and Chodera, John D and Schnieders, Michael J and Haque, Imran and Mobley, David L and Lambrecht, Daniel S and DiStasio Jr, Robert A and others},
-  journal={The journal of physical chemistry B},
+  journal={J. Phys. Chem. B},
   volume={114},
   number={8},
   pages={2549--2564},
@@ -1112,7 +1268,7 @@ @article{amoeba10
 @article{amoeba13,
   title={{Polarizable atomic multipole-based AMOEBA force field for proteins}},
   author={Shi, Yue and Xia, Zhen and Zhang, Jiajing and Best, Robert and Wu, Chuanjie and Ponder, Jay W and Ren, Pengyu},
-  journal={Journal of chemical theory and computation},
+  journal={J. Chem. Theory Comput.},
   volume={9},
   number={9},
   pages={4046--4063},
@@ -1123,7 +1279,7 @@ @article{amoeba13
 @article{amoeba06,
   title={Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure},
   author={Piquemal, Jean-Philip and Perera, Lalith and Cisneros, G Andr{\'e}s and Ren, Pengyu and Pedersen, Lee G and Darden, Thomas A},
-  journal={The Journal of chemical physics},
+  journal={J. Chem. Phys.},
   volume={125},
   number={5},
   pages={054511},
@@ -1147,7 +1303,7 @@ @article{thole1981
 @article{ren2003polarizable,
   title={Polarizable atomic multipole water model for molecular mechanics simulation},
   author={Ren, Pengyu and Ponder, Jay W},
-  journal={The Journal of Physical Chemistry B},
+  journal={J. Phys. Chem. B},
   volume={107},
   number={24},
   pages={5933--5947},
@@ -1159,7 +1315,7 @@ @article{ren2003polarizable
 @article{huang2017mapping,
   title={Mapping the Drude polarizable force field onto a multipole and induced dipole model},
   author={Huang, Jing and Simmonett, Andrew C and Pickard IV, Frank C and MacKerell Jr, Alexander D and Brooks, Bernard R},
-  journal={The Journal of chemical physics},
+  journal={J. Chem. Phys.},
   volume={147},
   number={16},
   pages={161702},
@@ -1398,7 +1554,7 @@ @article{berendsen1996
 doi = {10.1063/1.470992},
 isbn = {0021-9606},
 issn = {00219606},
-journal = {Journal of Chemical Physics},
+journal = {J. Chem. Phys.},
 mendeley-groups = {Marrink},
 month = {feb},
 number = {7},
@@ -1420,6 +1576,9 @@ @Article{catte16
 Pages = "32560-32569 "
 }
 
+%% REFERENCE TO BE UPDATED
+%  according to the current status at submittion
+%
 @Article{nmrlipids_proj4,
 author ="
 Amelie Bacle and
@@ -1467,13 +1626,12 @@ @Article{perspective_cecam_lugano_2018
 @article{melcr18,
 author = {Melcr, Josef and Martinez-Seara, Hector and Nencini, Ricky and Kolafa, Jiří and Jungwirth, Pavel and Ollila, O. H. Samuli},
 title = {Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization},
-journal = {The Journal of Physical Chemistry B},
+journal = {J. Phys. Chem. B},
 volume = {122},
 number = {16},
 pages = {4546-4557},
 year = {2018},
 doi = {10.1021/acs.jpcb.7b12510},
-    note ={PMID: 29608850},
 URL = { https://doi.org/10.1021/acs.jpcb.7b12510 },
 eprint = { https://doi.org/10.1021/acs.jpcb.7b12510 }
 ,
@@ -1505,7 +1663,7 @@ @article{melcr16
 @article{timr2018calcium,
   title={{Calcium Sensing by Recoverin: Effect of Protein Conformation on Ion Affinity}},
   author={Timr, {\v{S}}t{\v{e}}p{\'a}n and Kadlec, Jan and Srb, Pavel and Ollila, O. H. Samuli and Jungwirth, Pavel},
-  journal={The journal of physical chemistry letters},
+  journal={J. Phys. Chem. Lett.},
   volume={9},
   number={7},
   pages={1613--1619},
@@ -2199,7 +2357,7 @@ @article{Herbette84
 }
 
 @article{Pall13,
-title = "A flexible algorithm for calculating pair interactions on \{SIMD\} architectures ",
+title = "A flexible algorithm for calculating pair interactions on SIMD architectures ",
 journal = "Comput. Phys. Commun.",
 volume = "184",
 number = "12",
@@ -3776,7 +3934,7 @@ @article{roux90
 }
 
 @article{Roux91,
-title = "Calcium binding by phosphatidylserine headgroups. Deuterium \{NMR\} study ",
+title = "Calcium binding by phosphatidylserine headgroups. Deuterium NMR study ",
 journal = "Biophys. J. ",
 volume = "60",
 number = "1",
@@ -3946,7 +4104,7 @@ @article{harder2009
 doi = {10.1021/ja806825g},
 isbn = {1520-5126 (Electronic)$\backslash$n0002-7863 (Linking)},
 issn = {00027863},
-journal = {Journal of the American Chemical Society},
+journal = {J. Am. Chem. Soc.},
 mendeley-groups = {MD simulations - technics/polarizable simulations},
 month = {mar},
 number = {8},
@@ -4485,7 +4643,7 @@ @article{sachs04_potential
 doi = {10.1063/1.1826056},
 file = {:home/joe/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Sachs, Crozier, Woolf - 2004 - Atomistic simulations of biologically realistic transmembrane potential gradients.pdf:pdf},
 issn = {0021-9606},
-journal = {The Journal of chemical physics},
+journal = {J. Chem. Phys.},
 keywords = {Biophysics,Biophysics: methods,Computer Simulation,Dimyristoylphosphatidylcholine,Dimyristoylphosphatidylcholine: chemistry,Lipid Bilayers,Lipid Bilayers: chemistry,Membrane Potentials,Models,Molecular,Molecular Conformation,Software,Static Electricity,Statistical},
 mendeley-groups = {membranes,membranes/mempot},
 month = {dec},
@@ -4601,7 +4759,7 @@ @article{Roux1997
 author = {Roux, Beno{\^\i}t},
 file = {:home/joe/Documents/Mendeley Desktop/1997/1997 - Influence of the Membrane potential on the free energy of an intrinsic protein - Roux.pdf:pdf},
 isbn = {5143437105},
-journal = {Biophysical Journal},
+journal = {Biophys. J.},
 number = {December},
 pages = {2980--2989},
 title = {{Influence of the Membrane potential on the free energy of an intrinsic protein}},
@@ -4638,7 +4796,7 @@ @article{link1997comparing
 @article{urquhart1998comparison,
   title={{Comparison of Predicted and Observed Properties of Proteins Encoded in the Genome of Mycobacterium Tuberculosis H37Rv}},
   author={Urquhart, Brooke L and Cordwell, Stuart J and Humphery-Smith, Ian},
-  journal={Biochemical and biophysical research communications},
+  journal={Biochem. Biophys. Res. Commun.},
   volume={253},
   number={1},
   pages={70--79},
@@ -4826,7 +4984,7 @@ @article{Pluhackova2016
 doi = {10.1021/acs.jpcb.6b01870},
 isbn = {1520-6106},
 issn = {15205207},
-journal = {Journal of Physical Chemistry B},
+journal = {J. Phys. Chem. B},
 month = {apr},
 number = {16},
 pages = {3888--3903},
@@ -4906,7 +5064,7 @@ @article{Petrache06
 
 @article{parsegian89,
 title = "Hydration forces between phospholipid bilayers",
-journal = "Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes",
+journal = "Biochim. Biophys. Acta",
 volume = "988",
 number = "3",
 pages = "351 - 376",
@@ -4919,7 +5077,7 @@ @article{parsegian89
 
 @article{rappolt03,
 title = "Mechanism of the Lamellar/Inverse Hexagonal Phase Transition Examined by High Resolution X-Ray Diffraction",
-journal = "Biophysical Journal",
+journal = "Biophys. J.",
 volume = "84",
 number = "5",
 pages = "3111 - 3122",
@@ -5114,7 +5272,7 @@ @article{Garavito01
 number = {35}, 
 pages = {32403-32406}, 
 year = {2001},  
-journal = {Journal of Biological Chemistry} 
+journal = {J. Biol. Chem.} 
 }
 
 @article{Dvinskikh04,
@@ -5174,7 +5332,7 @@ @article{leaver01
 
 @Article{ferreira13,
 author ="Ferreira, Tiago Mendes and Coreta-Gomes, Filipe and Ollila, O. H. Samuli and Moreno, Maria Joao and Vaz, Winchil L. C. and Topgaard, Daniel",
-title  ="{{Cholesterol and POPC segmental order parameters in lipid membranes: solid state $^1$H-$^13$C NMR and MD simulation studies}}",
+title  ="{{Cholesterol and POPC segmental order parameters in lipid membranes: solid state $^1$H-$^{13}$C NMR and MD simulation studies}}",
 journal  ="Phys. Chem. Chem. Phys.",
 year  ="2013",
 volume  ="15",
@@ -10831,7 +10989,7 @@ @article{ye2018phosphatidylinositol
 @article {mdanalysis2011,
 author = {Michaud-Agrawal, Naveen and Denning, Elizabeth J. and Woolf, Thomas B. and Beckstein, Oliver},
 title = {MDAnalysis: A toolkit for the analysis of molecular dynamics simulations},
-journal = {Journal of Computational Chemistry},
+journal = {J. Comput. Chem.},
 volume = {32},
 number = {10},
 publisher = {Wiley Subscription Services, Inc., A Wiley Company},
diff --git a/img/POPCstructure_horiz.pdf b/img/POPCstructure_horiz.pdf
new file mode 100644
index 0000000..1d55fc5
Binary files /dev/null and b/img/POPCstructure_horiz.pdf differ
diff --git a/img/TOC_graphic.pdf b/img/TOC_graphic.pdf
new file mode 100644
index 0000000..70e3f79
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diff --git a/img/TOC_graphic.sla b/img/TOC_graphic.sla
new file mode 100644
index 0000000..b63d076
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similarity index 80%
rename from Fig/order_parameters_changes_A-B_PC-PS_mix_POPC_kcl.pdf
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similarity index 72%
rename from Fig/order_parameters_changes_A-B_PC-PS_mix_POPC_nacl.pdf
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similarity index 100%
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similarity index 100%
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new file mode 100644
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diff --git a/img/populations_stoichiometry_structures_SI.pdf b/img/populations_stoichiometry_structures_SI.pdf
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index 0000000..48fedbb
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diff --git a/img/stoichiometry_CaCl2_comparison_Ecc-lipids_PC-vs-PCPS.pdf b/img/stoichiometry_CaCl2_comparison_Ecc-lipids_PC-vs-PCPS.pdf
index e5b95eb..ace8f35 100644
Binary files a/img/stoichiometry_CaCl2_comparison_Ecc-lipids_PC-vs-PCPS.pdf and b/img/stoichiometry_CaCl2_comparison_Ecc-lipids_PC-vs-PCPS.pdf differ