refs.bib

@article{antila21a,
author = {Antila, Hanne S. and M. Ferreira, Tiago and Ollila, O. H. Samuli and Miettinen, Markus S.},
title = {Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics},
journal = {J.Chem. Inf. Model.},
volume = {61},
number = {2},
pages = {938-949},
year = {2021},
}

@article{buslaev16,
author = {Buslaev, Pavel and Gordeliy, Valentin and Grudinin, Sergei and Gushchin, Ivan},
title = {Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations},
journal = {J. Chem. Theory Comput.},
volume = {12},
number = {3},
pages = {1019-1028},
year = {2016},
}

@article{sormanni17,
author={Sormanni, Pietro
and Piovesan, Damiano
and Heller, Gabriella T.
and Bonomi, Massimiliano
and Kukic, Predrag
and Camilloni, Carlo
and Fuxreiter, Monika
and Dosztanyi, Zsuzsanna
and Pappu, Rohit V.
and Babu, M. Madan
and Longhi, Sonia
and Tompa, Peter
and Dunker, A. Keith
and Uversky, Vladimir N.
and Tosatto, Silvio C. E.
and Vendruscolo, Michele},
title={Simultaneous quantification of protein order and disorder},
journal={Nat. Chem. Biol.},
year={2017},
month={Apr},
day={01},
volume={13},
number={4},
pages={339-342},
}



@article{schoenmaker21,
title = {mRNA-lipid nanoparticle COVID-19 vaccines: Structure and stability},
journal = {International Journal of Pharmaceutics},
volume = {601},
pages = {120586},
year = {2021},
issn = {0378-5173},
doi = {https://doi.org/10.1016/j.ijpharm.2021.120586},
url = {https://www.sciencedirect.com/science/article/pii/S0378517321003914},
author = {Linde Schoenmaker and Dominik Witzigmann and Jayesh A. Kulkarni and Rein Verbeke and Gideon Kersten and Wim Jiskoot and Daan J.A. Crommelin},
keywords = {COVID-19, Lipid nanoparticle (LNP), Lyophilization, mRNA, Shelf life, Storage stability, Structure, Vaccine},
}

@article{pardi18,
author={Pardi, Norbert
and Hogan, Michael J.
and Porter, Frederick W.
and Weissman, Drew},
title={mRNA vaccines --- a new era in vaccinology},
journal={Nat. Rev. Drug Disc.},
year={2018},
month={Apr},
day={01},
volume={17},
number={4},
pages={261-279},
issn={1474-1784},
doi={10.1038/nrd.2017.243},
url={https://doi.org/10.1038/nrd.2017.243}
}



@article{harayama18,
author = {Harayama, T and Riezman, H},
title = {Understanding the diversity of membrane lipid composition},
journal = {Nat. Rev. Mol. Cell Biol.},
volume = {19},
number = {5},
Pages = {281-296},
year = {2018},
doi = {10.1038/nrm.2017.138},
URL = {https://doi.org/10.1038/nrm.2017.138}
}


@article{shirts17,
author={Shirts, Michael R.
and Klein, Christoph
and Swails, Jason M.
and Yin, Jian
and Gilson, Michael K.
and Mobley, David L.
and Case, David A.
and Zhong, Ellen D.},
title={Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset},
journal={Journal of Computer-Aided Molecular Design},
year={2017},
month={Jan},
day={01},
volume={31},
number={1},
pages={147-161},
}



@article{schmid11,
author={Schmid, Nathan
and Eichenberger, Andreas P.
and Choutko, Alexandra
and Riniker, Sereina
and Winger, Moritz
and Mark, Alan E.
and van Gunsteren, Wilfred F.},
title={Definition and testing of the GROMOS force-field versions 54A7 and 54B7},
journal={European Biophysics Journal},
year={2011},
month={Apr},
day={30},
volume={40},
number={7},
pages={843},
}



@article{pronk13,
    author = {Pronk, Sander and Páll, Szilárd and Schulz, Roland and Larsson, Per and Bjelkmar, Pär and Apostolov, Rossen and Shirts, Michael R. and Smith, Jeremy C. and Kasson, Peter M. and van der Spoel, David and Hess, Berk and Lindahl, Erik},
    title = "{GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit}",
    journal = {Bioinformatics},
    volume = {29},
    number = {7},
    pages = {845-854},
    year = {2013},
    month = {02},
}


@dataset{charmmPOPC313K,
  author       = {Ollila},
  title        = {POPC CHARMM36 T313K},
  month        = sep,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.4040423},
  url          = {https://doi.org/10.5281/zenodo.4040423}
}

@misc{POPClipid1450perCATsurfT313K,
  author       = {Ollila, O. H. Samuli},
  title        = {{POPC bilayer with 50\% of 
                   dihexadecyldimethylammonium simulated at T313K
                   with the Lipid14 model using Gromacs}},
  month        = oct,
  year         = 2017,
  doi          = {10.5281/zenodo.1020689},
  url          = {https://doi.org/10.5281/zenodo.1020689}
}

@misc{POPClipid1442perCATsurfT313K,
  author       = {Ollila, O. H. Samuli},
  title        = {{POPC bilayer with 42\% of 
                   dihexadecyldimethylammonium simulated at T313K
                   with the Lipid14 model using Gromacs}},
  month        = oct,
  year         = 2017,
  doi          = {10.5281/zenodo.1020671},
  url          = {https://doi.org/10.5281/zenodo.1020671}
}

@misc{POPClipid1430perCATsurfT313K,
  author       = {Ollila, O. H. Samuli},
  title        = {{POPC bilayer with 30\% of 
                   dihexadecyldimethylammonium simulated at T313K
                   with the Lipid14 model using Gromacs}},
  month        = oct,
  year         = 2017,
  doi          = {10.5281/zenodo.1020623},
  url          = {https://doi.org/10.5281/zenodo.1020623}
}

@misc{POPClipid1420perCATsurfT313K,
  author       = {Ollila, O. H. Samuli},
  title        = {{POPC bilayer with 20\% of 
                   dihexadecyldimethylammonium simulated at T313K
                   with the Lipid14 model using Gromacs}},
  month        = oct,
  year         = 2017,
  doi          = {10.5281/zenodo.1020593},
  url          = {https://doi.org/10.5281/zenodo.1020593}
}

@misc{POPClipid1410perCATsurfT313K,
  author       = {Ollila, O. H. Samuli},
  title        = {{POPC bilayer with 10\% of 
                   dihexadecyldimethylammonium simulated at T313K
                   with the Lipid14 model using Gromacs}},
  month        = oct,
  year         = 2017,
  doi          = {10.5281/zenodo.1020240},
  url          = {https://doi.org/10.5281/zenodo.1020240}
}

@misc{POPClipid14T313K,
  author       = {Ollila, O. H. Samuli},
  title        = {{POPC bilayer simulated at T313K with the Lipid14 
                   model using Gromacs}},
  month        = oct,
  year         = 2017,
  doi          = {10.5281/zenodo.1020709},
  url          = {https://doi.org/10.5281/zenodo.1020709}
}

@article{vigant15,
author={Vigant, Frederic
and Santos, Nuno C.
and Lee, Benhur},
title={Broad-spectrum antivirals against viral fusion},
journal={Nat. Rev. Microbiol.},
year={2015},
month={Jul},
day={01},
volume={13},
number={7},
pages={426-437},
}



@article{berendsen87,
author = {Berendsen, H. J. C. and Grigera, J. R. and Straatsma, T. P.},
title = {The missing term in effective pair potentials},
journal = {J. Phys. Chem.},
volume = {91},
number = {24},
pages = {6269-6271},
year = {1987},
}

@article{dijon20,
author = {Duboué-Dijon,E.  and Javanainen,M.  and Delcroix,P.  and Jungwirth,P.  and Martinez-Seara,H. },
title = {A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization},
journal = {J. Chem. Phys.},
volume = {153},
number = {5},
pages = {050901},
year = {2020},
}

@article{Pall13,
title = "A flexible algorithm for calculating pair interactions on \{SIMD\} architectures ",
journal = "Comput. Phys. Commun.",
volume = "184",
number = "12",
pages = "2641 - 2650",
year = "2013",
note = "",
issn = "0010-4655",
doi = "http://dx.doi.org/10.1016/j.cpc.2013.06.003",
author = "Szilárd P{\'a}ll and Berk Hess",
}


@misc{POPCPOPG73lipid17,
  author       = {Pe{\'o}n, Antonio},
  title        = {{LIPID17 POPC-POPG 7:3 Bilayer Simulation (Last 100 
                   ns, 150 mM NaCl, 310 K )}},
  month        = feb,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.2585523},
  url          = {https://doi.org/10.5281/zenodo.2585523}
}

@article{pall20,
author = {P{\'a}ll,Szilárd  and Zhmurov,Artem  and Bauer,Paul  and Abraham,Mark  and Lundborg,Magnus  and Gray,Alan  and Hess,Berk  and Lindahl,Erik },
title = {Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS},
journal = {J. Chem. Phys.},
volume = {153},
number = {13},
pages = {134110},
year = {2020},
}

@article{tanaka15,
author={Tanaka, Koji
and Caaveiro, Jose M.M.
and Morante, Koldo
and Gonz{\'a}lez-Ma{\~{n}}as, Juan Manuel
and Tsumoto, Kouhei},
title={Structural basis for self-assembly of a cytolytic pore lined by protein and lipid},
journal={Nat. Commun.},
year={2015},
month={Feb},
day={26},
volume={6},
number={1},
pages={6337},
abstract={Pore-forming toxins (PFT) are water-soluble proteins that possess the remarkable ability to self-assemble on the membrane of target cells, where they form pores causing cell damage. Here, we elucidate the mechanism of action of the haemolytic protein fragaceatoxin C (FraC), a $\alpha$-barrel PFT, by determining the crystal structures of FraC at four different stages of the lytic mechanism, namely the water-soluble state, the monomeric lipid-bound form, an assembly intermediate and the fully assembled transmembrane pore. The structure of the transmembrane pore exhibits a unique architecture composed of both protein and lipids, with some of the lipids lining the pore wall, acting as assembly cofactors. The pore also exhibits lateral fenestrations that expose the hydrophobic core of the membrane to the aqueous environment. The incorporation of lipids from the target membrane within the structure of the pore provides a membrane-specific trigger for the activation of a haemolytic toxin.},
issn={2041-1723},
doi={10.1038/ncomms7337},
url={https://doi.org/10.1038/ncomms7337}
}



@article{muramoto10,
	author = {Muramoto, Kazumasa and Ohta, Kazuhiro and Shinzawa-Itoh, Kyoko and Kanda, Katsumasa and Taniguchi, Maki and Nabekura, Hiroyuki and Yamashita, Eiki and Tsukihara, Tomitake and Yoshikawa, Shinya},
	title = {Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate},
	volume = {107},
	number = {17},
	pages = {7740--7745},
	year = {2010},
	doi = {10.1073/pnas.0910410107},
	publisher = {National Academy of Sciences},
	issn = {0027-8424},
	URL = {https://www.pnas.org/content/107/17/7740},
	eprint = {https://www.pnas.org/content/107/17/7740.full.pdf},
	journal = {Proc. Natl. Acad. Sci. U.S.A.}
}

@article{schaaf08,
author={Schaaf, Gabriel
and Ortlund, Eric A.
and Tyeryar, Kimberly R.
and Mousley, Carl J.
and Ile, Kristina E.
and Garrett, Teresa A.
and Ren, Jihui
and Woolls, Melissa J.
and Raetz, Christian R.H.
and Redinbo, Matthew R.
and Bankaitis, Vytas A.},
title={Functional Anatomy of Phospholipid Binding and Regulation of Phosphoinositide Homeostasis by Proteins of the Sec14 Superfamily},
journal={Mol. Cell},
year={2008},
month={Feb},
day={01},
publisher={Elsevier},
volume={29},
number={2},
pages={191-206},
issn={1097-2765},
doi={10.1016/j.molcel.2007.11.026},
url={https://doi.org/10.1016/j.molcel.2007.11.026}
}



@article{huang05,
title = {Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial bc1 Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-bonding Pattern},
journal = {J. Mol. Biol.},
volume = {351},
number = {3},
pages = {573-597},
year = {2005},
issn = {0022-2836},
doi = {https://doi.org/10.1016/j.jmb.2005.05.053},
url = {https://www.sciencedirect.com/science/article/pii/S0022283605006078},
author = {L. Huang and David Cobessi and Eric Y. Tung and Edward A. Berry},
keywords = {cytochrome , antimycin, respiratory chain, membrane protein complex, inhibitor binding site},
}

@article{mcgibbon15,
    title = {MDTraj: A Modern Open Library for the Analysis of
    Molecular Dynamics Trajectories},
    author = {McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan,
    Matthew P. and Klein, Christoph and Swails, Jason M. and
    Hern{\'a}ndez, Carlos X.  and Schwantes, Christian R. and Wang,
    Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
    journal = {Biophys. J.},
    volume = {109},
    number = {8},
    pages = {1528 -- 1532},
    year = {2015},
    doi = {10.1016/j.bpj.2015.08.015}
}

@misc{antila21b,
      title={Quasi-uncoupled rotational diffusion of phospholipid headgroups from the main molecular frame}, 
      author={Hanne S. Antila and Anika Wurl and O. H. Samuli Ollila and Markus S. Miettinen and Tiago M. Ferreira},
      year={2020},
      eprint={2009.06774},
      archivePrefix={arXiv},
      primaryClass={cond-mat.soft}
}

@article{lee11,
  doi = {10.1016/j.tibs.2011.06.007},
  url = {https://doi.org/10.1016/j.tibs.2011.06.007},
  year = {2011},
  month = sep,
  publisher = {Elsevier {BV}},
  volume = {36},
  number = {9},
  pages = {493--500},
  author = {Anthony G. Lee},
  title = {Biological membranes: the importance of molecular detail},
  journal = {Trends Biochem. Sci.}
}

@article{marsh13b,
  doi = {10.1007/s00249-012-0816-6},
  url = {https://doi.org/10.1007/s00249-012-0816-6},
  year = {2013},
  month = may,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {42},
  number = {2-3},
  pages = {119--146},
  author = {Derek Marsh and Tibor P{\'{a}}li},
  title = {Orientation and conformation of lipids in crystals of transmembrane proteins},
  journal = {Eur. Biophys. J.}
}

@article{pezeshkian18,
title = "Lipid Configurations from Molecular Dynamics Simulations",
journal = "Biophys. J.",
volume = "114",
number = "8",
pages = "1895 - 1907",
year = "2018",
issn = "0006-3495",
doi = "https://doi.org/10.1016/j.bpj.2018.02.016",
url = "http://www.sciencedirect.com/science/article/pii/S0006349518302467",
author = "Weria Pezeshkian and Himanshu Khandelia and Derek Marsh",
}

@article{akutsu20,
  doi = {10.1016/j.bbamem.2020.183352},
  url = {https://doi.org/10.1016/j.bbamem.2020.183352},
  year = {2020},
  month = sep,
  publisher = {Elsevier {BV}},
  volume = {1862},
  number = {9},
  pages = {183352},
  author = {Hideo Akutsu},
  title = {Structure and dynamics of phospholipids in membranes elucidated by combined use of {NMR} and vibrational spectroscopies},
  journal = {Biochim. Biophys. Acta}
}

@article{vanmeer08,
  doi = {10.1038/nrm2330},
  url = {https://doi.org/10.1038/nrm2330},
  year = {2008},
  month = feb,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {9},
  number = {2},
  pages = {112--124},
  author = {Gerrit van Meer and Dennis R. Voelker and Gerald W. Feigenson},
  title = {Membrane lipids: where they are and how they behave},
  journal = {Nat. Rev. Mol. Cell Biol.}
}

@article{lee03,
title = "Lipid--protein interactions in biological membranes: a structural perspective",
journal = "Biochim. Biophys. Acta",
volume = "1612",
number = "1",
pages = "1 - 40",
year = "2003",
issn = "0005-2736",
doi = "https://doi.org/10.1016/S0005-2736(03)00056-7",
url = "http://www.sciencedirect.com/science/article/pii/S0005273603000567",
author = "A.G Lee",
keywords = "Annular lipid, Non-annular site, Hydrophobic mismatch, Membrane protein structure, Lipid bilayer, Lipid–protein interaction, Membrane structure",
}

@dataset{Lipid17eccPOPCPOPG80201000mMCaCl,
  author       = {Anne M. Kiirikki and O. H. Samuli Ollila},
  title        = {{Lipid17ecc POPC:POPG 4:1 bilayer simulation in 1 M 
                   CaCl2 solution and Na+ counter ions}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.4492639},
  url          = {https://doi.org/10.5281/zenodo.4492639}
}

@dataset{Lipid17eccPOPCPOPG8020100mMCaCl,
  author       = {Anne M. Kiirikki and O. H. Samuli Ollila},
  title        = {{Lipid17ecc POPC:POPG 4:1 bilayer simulation in 0.1 
                   M CaCl2 solution and Na+ counter ions}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3997176},
  url          = {https://doi.org/10.5281/zenodo.3997176}
}

@dataset{Lipid17eccPOPCPOPG8020,
  author       = {Anne M. Kiirikki and O. H. Samuli Ollila},
  title        = {{Lipid17ecc POPC:POPG 4:1 MD simulation  in water 
                   with Na+ counter ions}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3997154},
  url          = {https://doi.org/10.5281/zenodo.3997154}
}

@article{berman00,
    author = {Berman, Helen M. and Westbrook, John and Feng, Zukang and Gilliland, Gary and Bhat, T. N. and Weissig, Helge and Shindyalov, Ilya N. and Bourne, Philip E.},
    title = "{The Protein Data Bank}",
    journal = {Nucleic Acids Res.},
    volume = {28},
    number = {1},
    pages = {235-242},
    year = {2000},
    month = {01},
    abstract = "{The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.}",
    issn = {0305-1048},
    doi = {10.1093/nar/28.1.235},
    url = {https://doi.org/10.1093/nar/28.1.235},
    eprint = {https://academic.oup.com/nar/article-pdf/28/1/235/9895144/280235.pdf},
}


@dataset{Lipid17POPCPOPG80201000mMCaCl,
  author       = {Virtanen, Salla and
                  Ollila, O. H. Samuli},
  title        = {{LIPID17 POPC-POPG 80:20 MD simulation, Na+ 
                   counterions and 1000mM CaCl2, 298K}},
  month        = oct,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3874378},
  url          = {https://doi.org/10.5281/zenodo.3874378}
}

@dataset{Lipid17POPCPOPG5050100mMCaCl,
  author       = {Virtanen, Salla and
                  Ollila, O. H. Samuli},
  title        = {{LIPID17 POPC-POPG 50:50 MD simulation, Na+ 
                   counterions and 100mM CaCl2, 298K}},
  month        = oct,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3871590},
  url          = {https://doi.org/10.5281/zenodo.3871590}
}

@dataset{Lipid17POPCPOPG50501000mMCaCl,
  author       = {Virtanen, Salla and
                  Ollila, O. H. Samuli},
  title        = {{LIPID17 POPC-POPG 50:50 MD simulation, Na+ 
                   counterions and 1000mM CaCl2, 298K}},
  month        = oct,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3864993},
  url          = {https://doi.org/10.5281/zenodo.3864993}
}

@dataset{Lipid17eccPOPCPOPG50501000mMCaCl,
  author       = {Ollila, O. H. Samuli and
                  Virtanen, I. Salla},
  title        = {{ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ 
                   counterions and 1000mM CaCl2, 298K}},
  month        = may,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3862036},
  url          = {https://doi.org/10.5281/zenodo.3862036}
}

@dataset{Lipid17eccPOPCPOPG5050,
  author       = {Ollila, O. H. Samuli and
                  Virtanen, I. Salla},
  title        = {{ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ 
                   counterions, 298K}},
  month        = may,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3859339},
  url          = {https://doi.org/10.5281/zenodo.3859339}
}

@dataset{Lipid17eccPOPCPOPG5050100mMCaCl,
  author       = {Ollila, O. H. Samuli and
                  Virtanen, I. Salla},
  title        = {{ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ 
                   counterions and 100mM CaCl2, 298K}},
  month        = may,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3855729},
  url          = {https://doi.org/10.5281/zenodo.3855729}
}

@article{kohagen16,
author = {Miriam Kohagen and Philip E. Mason and Pavel Jungwirth},
title = {Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering},
journal = {J. Phys. Chem. B},
volume = {120},
number = {8},
pages = {1454-1460},
year = {2016},
}

@article{martinek18,
  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={J. Chem. Phys.},
  volume={148},
  number={22},
  pages={222813},
  year={2018},
  publisher={AIP Publishing}
}

@article{pluharova14,
author = {Pluha{\v r}ov{\'{a}}, Eva and Fischer, Henry E. and Mason, Philip E. and Jungwirth, Pavel},
doi = {10.1080/00268976.2013.875231},
issn = {0026-8976},
journal = {Mol. Phys.},
keywords = {chloride,lithium,molecular dynamics,neutron scattering,solution},
language = {en},
month = {jan},
number = {9-10},
pages = {1230--1240},
publisher = {Taylor {\&} Francis},
title = {{Hydration of the chloride ion in concentrated aqueous solutions using neutron scattering and molecular dynamics}},
url = {http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.875231},
volume = {112},
year = {2014}
}

@dataset{Lipid17POPCPOPG8020100mMCaCl,
  author       = {Virtanen, Salla and
                  Ollila, O. H. Samuli},
  title        = {{LIPID17 POPC-POPG 80:20 MD simulation, Na+ 
                   counterions and 100mM CaCl2, 298K}},
  month        = oct,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3833725},
  url          = {https://doi.org/10.5281/zenodo.3833725}
}

@misc{POPC7POPG3gromosCKPT310K,
  author       = {Pe{\'o}n, Antonio},
  title        = {{GROMOS-CKP POPC-POPG 7:3 Bilayer Simulation (Last 
                   100 ns,  310 K )}},
  month        = jul,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3266240},
  url          = {https://doi.org/10.5281/zenodo.3266240}
}

@misc{POPCgromosCKPT310K,
  author       = {Pe{\'o}n, Antonio},
  title        = {{GROMOS-CKP POPC Bilayer Simulation (Last 100 ns, 
                   310 K )}},
  month        = jun,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3247435},
  url          = {https://doi.org/10.5281/zenodo.3247435}
}

@dataset{POPCslipid298K,
  author       = {Favela-Rosales, Fernando},
  title        = {{MD simulation trajectory of a lipid bilayer: Pure 
                   POPC in water. SLIPIDS, Gromacs 4.6.3. 2016.}},
  month        = nov,
  year         = 2016,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.166034},
  url          = {https://doi.org/10.5281/zenodo.166034}
}

@dataset{POPC1POPE1slipidT298K,
  author       = {Javanainen, Matti},
  title        = {{Simulation of POPC:POPE 1:1 membrane with the 
                   Slipids force field}},
  month        = jan,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3605386},
  url          = {https://doi.org/10.5281/zenodo.3605386}
}

@dataset{POPC1POPE1macrogT300K,
  author       = {Mil{\'a}n Rodr{\'i}guez, Paula and
                  Fuchs, Patrick F. J.},
  title        = {{MacRog POPC/POPE 1:1 MD simulation (300 K -  500ns 
                   - 1 bar)}},
  month        = mar,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3725637},
  url          = {https://doi.org/10.5281/zenodo.3725637}
}

@dataset{POPCmacrog300K,
  author       = {Mil{\'a}n Rodr{\'i}guez, Paula and
                  Fuchs, Patrick F. J.},
  title        = {{MacRog pure POPC MD simulation (300 K - 500ns - 1 
                   bar)}},
  month        = apr,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3741793},
  url          = {https://doi.org/10.5281/zenodo.3741793}
}



@dataset{MacRogPOPEfilesT300K,
  author       = {Milan Rodriguez, Paula and
                  Fuchs, Patrick F.J.},
  title        = {{MacRog pure POPE MD simulation (300 K -  500ns - 1 
                   bar)}},
  month        = mar,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3725670},
  url          = {https://doi.org/10.5281/zenodo.3725670}
}

@misc{POPCslipid301K,
  author       = {Pe{\'o}n, Antonio},
  title        = {{SLIPID POPC Bilayer Simulation (Last 100 ns, 310 K 
                   )}},
  month        = may,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3235552},
  url          = {https://doi.org/10.5281/zenodo.3235552}
}

@Article{leontyev11,
author ="Leontyev, Igor and Stuchebrukhov, Alexei",
title  ="Accounting for electronic polarization in non-polarizable force fields",
journal  ="Phys. Chem. Chem. Phys.",
year  ="2011",
volume  ="13",
issue  ="7",
pages  ="2613-2626",
}

@dataset{slipidPOPC50POPG50T298K,
  author       = {Javanainen, Matti},
  title        = {{Simulations of POPC:POPG 1:1 membranes with 
                   varying levels of CaCl\_2 using the Slipids force
                   field}},
  month        = jan,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3613573},
  url          = {https://doi.org/10.5281/zenodo.3613573}
}

@misc{slipidPOPC70POPG30T310K,
  author       = {Pe{\'o}n, Antonio},
  title        = {{SLIPID POPC-POPG 7:3 Bilayer Simulation (Last 100 
                   ns, 310 K )}},
  month        = jun,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3240156},
  url          = {https://doi.org/10.5281/zenodo.3240156}
}

@dataset{Lipid17POPCPOPG8020,
  author       = {Virtanen, Salla and
                  Ollila, O. H. Samuli},
  title        = {{LIPID17 POPC-POPG 80:20 MD simulation, Na+ 
                   counterions, 298K}},
  month        = oct,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3693681},
  url          = {https://doi.org/10.5281/zenodo.3693681}
}

@dataset{Lipid17POPCPOPG5050,
  author       = {Virtanen, Salla and
                  Ollila, O. H. Samuli},
  title        = {{LIPID17 POPC-POPG 50:50 MD simulation, Na+ 
                   counterions, 298K}},
  month        = oct,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3857816},
  url          = {https://doi.org/10.5281/zenodo.3857816}
}

@dataset{MacRogPOPEfiles,
  author       = {Matti Javanainen},
  title        = {{Simulation of a POPE bilayer, lipid model based on 
                   OPLS-aa by Rog et al.}},
  month        = dec,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3571071},
  url          = {https://doi.org/10.5281/zenodo.3571071}
}

@article{tocanne90,
title = "Ionization of phospholipids and phospholipid-supported interfacial lateral diffusion of protons in membrane model systems ",
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volume = "1031",
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pages = "111 - 142",
year = "1990",
author = "Jean-François Tocanne and Justin Teissi{\'e}"
}

@article{marra85,
author = {Marra, Johan and Israelachvili, Jacob},
title = {Direct measurements of forces between phosphatidylcholine and phosphatidylethanolamine bilayers in aqueous electrolyte solutions},
journal = {Biochemistry},
volume = {24},
number = {17},
pages = {4608-4618},
year = {1985},
}


@article{devries04,
author = {de Vries, Alex H. and Mark, Alan E. and Marrink, Siewert J.},
title = {The Binary Mixing Behavior of Phospholipids in a Bilayer: A Molecular Dynamics Study},
journal = {The Journal of Physical Chemistry B},
volume = {108},
number = {7},
pages = {2454-2463},
year = {2004},
}


@article{tsai12,
title = "Molecular dynamics simulation of cation–phospholipid clustering in phospholipid bilayers: Possible role in stalk formation during membrane fusion",
journal = "Biochimica et Biophysica Acta (BBA) - Biomembranes",
volume = "1818",
number = "11",
pages = "2742 - 2755",
year = "2012",
issn = "0005-2736",
doi = "https://doi.org/10.1016/j.bbamem.2012.05.029",
url = "http://www.sciencedirect.com/science/article/pii/S0005273612001873",
author = "Hui-Hsu Gavin Tsai and Wei-Xiang Lai and Hong-Da Lin and Jian-Bin Lee and Wei-Fu Juang and Wen-Hsin Tseng",
keywords = "Cation–phospholipid clustering, Lipid bilayers property, Membrane fusion, Microdomain formation, Cation effect, Molecular dynamics simulation",
}

@article{zhao07,
title = "Atomic-Scale Structure and Electrostatics of Anionic Palmitoyloleoylphosphatidylglycerol Lipid Bilayers with Na+ Counterions",
journal = "Biophysical Journal",
volume = "92",
number = "4",
pages = "1114 - 1124",
year = "2007",
issn = "0006-3495",
doi = "https://doi.org/10.1529/biophysj.106.086272",
url = "http://www.sciencedirect.com/science/article/pii/S0006349507709232",
author = "Wei Zhao and Tomasz Róg and Andrey A. Gurtovenko and Ilpo Vattulainen and Mikko Karttunen",
}

@article{murzyn05,
title = "Phosphatidylethanolamine-Phosphatidylglycerol Bilayer as a Model of the Inner Bacterial Membrane",
journal = "Biophysical Journal",
volume = "88",
number = "2",
pages = "1091 - 1103",
year = "2005",
issn = "0006-3495",
doi = "https://doi.org/10.1529/biophysj.104.048835",
url = "http://www.sciencedirect.com/science/article/pii/S0006349505731799",
author = "Krzysztof Murzyn and Tomasz Róg and Marta Pasenkiewicz-Gierula",
}


@article{berglund15,
    author = {Berglund, Nils A. AND Piggot, Thomas J. AND Jefferies, Damien AND Sessions, Richard B. AND Bond, Peter J. AND Khalid, Syma},
    journal = {PLOS Computational Biology},
    publisher = {Public Library of Science},
    title = {Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study},
    year = {2015},
    month = {04},
    volume = {11},
    url = {https://doi.org/10.1371/journal.pcbi.1004180},
    pages = {1-17},
    number = {4},
    doi = {10.1371/journal.pcbi.1004180}
}

@article{yeagle14,
title = "Non-covalent binding of membrane lipids to membrane proteins",
journal = "Biochim. Biophys. Acta",
volume = "1838",
number = "6",
pages = "1548 - 1559",
year = "2014",
author = "Philip L. Yeagle",
}

@article{hariharan18,
author="Hariharan, Parameswaran
 and Tikhonova, Elena
 and Medeiros-Silva, João
 and Jeucken, Aike
 and Bogdanov, Mikhail V.
 and Dowhan, William
 and Brouwers, Jos F.
 and Weingarth, Markus
 and Guan, Lan
",
title="Structural and functional characterization of protein--lipid interactions of the Salmonella typhimurium melibiose transporter MelB",
journal=" BMC Biology",
year="2018",
volume="16",
pages="85",
}

@article{furse17,
author="Furse, Samuel",
title="Is phosphatidylglycerol essential for terrestrial life?",
journal="Journal of Chemical Biology",
year="2017",
month="Jan",
day="01",
volume="10",
number="1",
pages="1--9",
}

@article{vance15,
author = {Vance, Jean E.},
title = {Phospholipid Synthesis and Transport in Mammalian Cells},
journal = {Traffic},
volume = {16},
number = {1},
pages = {1-18},
year = {2015}
}


@article{patel17,
author = {Patel, Dhaval and Witt, Stephan N.},
Title = {Ethanolamine and Phosphatidylethanolamine: Partners in Health and Disease},
journal = {Oxid. Med. Cell. Longev.},
volume = {2017},
pages = {4829180},
year = {2017},
}

@article{calzada16,
title = "Phosphatidylethanolamine Metabolism in Health and Disease",
journal = "Int. Rev. Cell Mol. Biol.",
publisher = "Academic Press",
volume = "321",
pages = "29 - 88",
year = "2016",
author = "Elizabeth Calzada and Ouma Onguka and Steven M. Claypool",
}

@article{piggot17,
author = {Piggot, Thomas J. and Allison, Jane R. and Sessions, Richard B. and Essex, Jonathan W.},
Title = {On the Calculation of Acyl Chain Order Parameters from Lipid Simulations},
journal = {J. Chem. Theory Comput.},
volume = {13},
number = {11},
pages = {5683-5696},
year = {2017},
}

@article{antila19,
author = {Antila, Hanne and Buslaev, Pavel and Favela-Rosales, Fernando and Ferreira, Tiago M. and Gushchin, Ivan and Javanainen, Matti and Kav, Batuhan and Madsen, Jesper J. and Melcr, Josef and Miettinen, Markus S. and Määttä, Jukka and Nencini, Ricky and Ollila, O. H. Samuli and Piggot, Thomas J.},
title = {Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers},
journal = {J. Phys. Chem. B},
volume = {123},
number = {43},
pages = {9066-9079},
year = {2019},
}

@article{melcr20,
author = {Melcr, Josef and Ferreira, Tiago M. and Jungwirth, Pavel and Ollila, O. H. Samuli},
title = {Improved Cation Binding to Lipid Bilayers with Negatively Charged POPS by Effective Inclusion of Electronic Polarization},
journal = {J. Chem. Theo. Comput.},
volume = {16},
number = {1},
pages = {738-748},
year = {2020},
}

@article{sohlenkamp16,
    author = {Sohlenkamp, Christian and Geiger, Otto},
    title = "{Bacterial membrane lipids: diversity in structures and pathways}",
    journal = {FEMS Microbiol. Rev.},
    volume = {40},
    number = {1},
    pages = {133-159},
    year = {2015},
    month = {04},
}



@dataset{CHARMM36POPCPOPG40101000mMCaCl,
  author       = {Anne M. Kiirikki and O. H. Samuli Ollila},
  title        = {{POPC:POPG 4:1 MD simulation with CHARMM36 in 1 M 
                   CaCL2 solution with Na+ counterions}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3997037},
  url          = {https://doi.org/10.5281/zenodo.3997037}
}

@dataset{CHARMM36POPCPOPG4010100mMCaCl,
  author       = {Anne M. Kiirikki and O. H. Samuli Ollila},
  title        = {{POPC:POPG 4:1 MD simulation with CHARMM36 in 0.1 M 
                   CaCL2 solution with Na+ counter ions}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3997019},
  url          = {https://doi.org/10.5281/zenodo.3997019}
}

@dataset{CHARMM36POPCPOPG4010,
  author       = {Anne M. Kiirikki and O. H. Samuli Ollila},
  title        = {{POPC:POPG 4:1 MD simulation with CHARMM36 in water 
                   with Na+ counter ions}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3996952},
  url          = {https://doi.org/10.5281/zenodo.3996952}
}

@dataset{CHARMM36POPCPOPG5050100mMCaCl,
  author       = {Anne M. Kiirikki and O. H. Samuli Ollila},
  title        = {{POPC:POPG 1:1 MD simulation with CHARMM36 in 0.1 M 
                   CaCL solution and Na+ counter ions}},
  month        = sep,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.4005515},
  url          = {https://doi.org/10.5281/zenodo.4005515}
}

@dataset{CHARMM36POPCPOPG50501000mMCaCl,
  author       = {Anne M. Kiirikki and O. H. Samuli Ollila},
  title        = {{POPC:POPG 1:1 MD simulation with CHARMM36 in 1 M 
                   CaCL solution and Na+ counter ions}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3997135},
  url          = {https://doi.org/10.5281/zenodo.3997135}
}

@dataset{CHARMM36POPCPOPG5050150mMCaCl,
  author       = {Jesper J. Madsen},
  title        = {{MD simulations of bilayers containing PC/PG 
                   mixtures and CaCl\_2: 250POPC\_250POPG\_0.15MCaCl\_2}},
  month        = oct,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3483789},
  url          = {https://doi.org/10.5281/zenodo.3483789}
}

@dataset{CHARMM36POPCPOPG5050,
  author       = {Anne M. Kiirikki and O. H. Samuli Ollila},
  title        = {{POPC:POPG 1:1 MD simulation with CHARMM36 in water and Na+ counter ions}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3997116},
  url          = {https://doi.org/10.5281/zenodo.3997116}
}

@article{pan12b,
title = "Molecular structures of fluid phase phosphatidylglycerol bilayers as determined by small angle neutron and X-ray scattering",
journal = "Biochimica et Biophysica Acta (BBA) - Biomembranes",
volume = "1818",
number = "9",
pages = "2135 - 2148",
year = "2012",
author = "Jianjun Pan and Frederick A. Heberle and Stephanie Tristram-Nagle and Michelle Szymanski and Mary Koepfinger and John Katsaras and Norbert Kučerka",
}

@misc{gromosCKPpopeT310150mMNaCl,
  author       = {Pe{\'o}n, Antonio},
  title        = {{Gromos POPE Bilayer Simulation (Last 100 ns, 150 
                   mM NaCl, 310 K )}},
  month        = feb,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.2574491},
  url          = {https://doi.org/10.5281/zenodo.2574491}
}

@misc{POPElipid17,
  author       = {Pe{\'o}n, Antonio},
  title        = {{LIPID17 POPE  Bilayer Simulation (Last 100 ns, 310 
                   K ) using dihedral 9}},
  month        = jun,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.4424292},
  url          = {https://doi.org/10.5281/zenodo.4424292}
}


@misc{POPGslipids,
  author       = {Peón, Antonio},
  title        = {{LIPID17 POPG Bilayer Simulation (Last 100 ns,  310 K ) using dihedral type 9}},
  month        = jun,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3832274},
  url          = {https://doi.org/10.5281/zenodo.3832274}
}

@misc{POPGlipid17,
  author       = {Peón, Antonio},
  title        = {{LIPID17 POPG Bilayer Simulation (Last 100ns, 310 
                   K) using dihedral type 9 instead of type 1.}},
  month        = may,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3832219},
  url          = {https://doi.org/10.5281/zenodo.3832219}
}

@misc{POPGgromosCKP,
  author       = {Pe{\'o}n, Antonio},
  title        = {{GROMOS POPG Bilayer Simulation (Last 100 ns, 310 K 
                   )}},
  month        = jun,
  year         = 2019,
  doi          = {10.5281/zenodo.3266166},
  url          = {https://doi.org/10.5281/zenodo.3266166}
}

@misc{POPGcharmm,
  author       = {Pe{\'o}n, Antonio},
  title        = {{CHARMM36 POPG Bilayer Simulation (Last 100 ns, 310 
                   K )}},
  month        = jun,
  year         = 2019,
  doi          = {10.5281/zenodo.3237463},
  url          = {https://doi.org/10.5281/zenodo.3237463}
}

@misc{POPGgromosCKP150mMNaCl,
  author       = {PEÓN, Antonio},
  title        = {{Gromos POPG Bilayer Simulation (Last 100 ns, 150 
                   mM NaCl, 310 K )}},
  month        = feb,
  year         = 2019,
  doi          = {10.5281/zenodo.3257649},
  url          = {https://doi.org/10.5281/zenodo.3257649}
}

@misc{POPEslipids,
  author       = {Pe{\'o}n, Antonio},
  title        = {{SLIPID POPE Bilayer Simulation (Last 100 ns, 310 K 
                   )}},
  month        = may,
  year         = 2019,
  doi          = {10.5281/zenodo.3231342},
  url          = {https://doi.org/10.5281/zenodo.3231342}
}

@misc{gromosCKPpopeT310,
  author       = {Pe{\'o}n, Antonio},
  title        = {{GROMOS POPE Bilayer Simulation (Last 100 ns, 310 K 
                   )}},
  month        = jun,
  year         = 2019,
  doi          = {10.5281/zenodo.3237754},
  url          = {https://doi.org/10.5281/zenodo.3237754}
}

@misc{POPEcharmm,
  author       = {Pe{\'o}n, Antonio},
  title        = {{CHARMM36 POPE Bilayer Simulation (Last 100 ns, 310 
                   K )}},
  month        = jun,
  year         = 2019,
  doi          = {10.5281/zenodo.3237461},
  url          = {https://doi.org/10.5281/zenodo.3237461}
}

@misc{POPElipid17150mMNaCl,
  author       = {PEÓN, Antonio},
  title        = {{LIPID17 POPE Bilayer Simulation (Last 100 ns, 150 
                   mM NaCl, 310 K ) using dihedral 9}},
  month        = feb,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.4424934},
  url          = {https://doi.org/10.5281/zenodo.4424934}
}

@misc{POPGlipid17150mMNaCl,
  author       = {PEÓN, Antonio},
  title        = {{LIPID17 POPG Bilayer Simulation (Last 100 ns, 150 
                   mM NaCl, 310 K ) using dihedral type 9}},
  month        = feb,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.4386514},
  url          = {https://doi.org/10.5281/zenodo.4386514}
}


@misc{charmm36POPEfiles,
  author       = {Javanainen, Matti},
  title        = {{Simulation of a POPE bilayer at 310K with the 
                   CHARMM36 force field}},
  month        = apr,
  year         = 2019,
  doi          = {10.5281/zenodo.2641987},
  url          = {https://doi.org/10.5281/zenodo.2641987}
}

@misc{POPCslipid150mMNaCl301K,
  author       = {PEÓN, Antonio},
  title        = {{SLIPID POPC Bilayer Simulation (Last 100 ns, 150 
                   mM NaCl, 310 K )}},
  month        = feb,
  year         = 2019,
  doi          = {10.5281/zenodo.2574689},
  url          = {https://doi.org/10.5281/zenodo.2574689}
}

@misc{POPC7POPG1charmm36NaCl,
  author       = {Pe{\'o}n, Antonio},
  title        = {{CHARMM36 POPC-POPG 7:3 Bilayer Simulation (Last 
                   100 ns,  310 K )}},
  month        = jun,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3248689},
  url          = {https://doi.org/10.5281/zenodo.3248689}
}

@misc{POPC7POPG1charmm36,
  author       = {Pe{\'o}n, Antonio},
  title        = {{CHARMM36 POPC-POPG 7:3 Bilayer Simulation (Last 
                   100 ns,  310 K )}},
  month        = jun,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3248689},
  url          = {https://doi.org/10.5281/zenodo.3248689}
}

@misc{POPCcharmm150mMNaCl301K,
  author       = {Peón, Antonio},
  title        = {{CHARMM36 POPC Bilayer Simulation (Last 100 ns, 150 
                   mM NaCl, 310 K )}},
  month        = feb,
  year         = 2019,
  doi          = {10.5281/zenodo.2628335},
  url          = {https://doi.org/10.5281/zenodo.2628335}
}

@misc{POPCcharmmT310K,
  author       = {Pe{\'o}n, Antonio},
  title        = {{CHARMM36 POPC Bilayer Simulation (Last 100 ns, 310 
                   K )}},
  month        = jun,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3247813},
  url          = {https://doi.org/10.5281/zenodo.3247813}
}

@misc{POPEslipids150mMNaCl,
  author       = {PEÓN, Antonio},
  title        = {{SLIPID POPE Bilayer Simulation (Last 100 ns, 150 
                   mM NaCl, 310 K )}},
  month        = feb,
  year         = 2019,
  doi          = {10.5281/zenodo.2578069},
  url          = {https://doi.org/10.5281/zenodo.2578069}
}

@misc{POPEcharmm150mMNaCl,
  author       = {PEÓN, ANTONIO},
  title        = {{CHARMM36 POPE Bilayer Simulation (Last 100 ns, 150 
                   mM NaCl, 310 K )}},
  month        = feb,
  year         = 2019,
  doi          = {10.5281/zenodo.2577454},
  url          = {https://doi.org/10.5281/zenodo.2577454}
}

@misc{POPGcharmm150mMNaCl,
  author       = {PEÓN, Antonio},
  title        = {{CHARMM36 POPG Bilayer Simulation (Last 100 ns, 150 
                   mM NaCl, 310 K )}},
  month        = feb,
  year         = 2019,
  doi          = {10.5281/zenodo.2573531},
  url          = {https://doi.org/10.5281/zenodo.2573531}
}

@misc{POPGslipids150mMNaCl,
  author       = {PEÓN, Antonio},
  title        = {{SLIPID POPG Bilayer Simulation (Last 100 ns, 150 
                   mM NaCl, 310 K )}},
  month        = feb,
  year         = 2019,
  doi          = {10.5281/zenodo.2633773},
  url          = {https://doi.org/10.5281/zenodo.2633773}
}

@misc{CHARMM36popg,
  author       = {Ollila, O. H. Samuli},
  title        = {{POPG lipid bilayer simulation at T298K ran with 
                   MODEL\_CHARMM\_GUI force field and Gromacs}},
  month        = oct,
  year         = 2017,
  doi          = {10.5281/zenodo.1011096},
  url          = {https://doi.org/10.5281/zenodo.1011096}
}

@misc{gromosCKPdppe,
  author       = {Thomas Piggot},
  title        = {{GROMOS-CKP DPPE Simulations (versions 1 and 2) 342 
                   K}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293957},
  url          = {https://doi.org/10.5281/zenodo.1293957}
}

@misc{gromosCKPdope,
  author       = {Thomas Piggot},
  title        = {{GROMOS-CKP DOPE Simulations (versions 1 and 2) 271 
                   K}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293941},
  url          = {https://doi.org/10.5281/zenodo.1293941}
}

@misc{gromosCKPpope,
  author       = {Thomas Piggot},
  title        = {{GROMOS-CKP POPE Simulations (versions 1 and 2) 313 
                   K}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293932},
  url          = {https://doi.org/10.5281/zenodo.1293932}
}

@misc{berger2DOPEfiles,
  author       = {Thomas Piggot},
  title        = {{Berger DOPE Simulations (versions 1 and 2) 271 K - 
                   larger repulsive H}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293905},
  url          = {https://doi.org/10.5281/zenodo.1293905}
}

@misc{bergerDOPEfiles,
  author       = {Thomas Piggot},
  title        = {{Berger DOPE Simulations (versions 1 and 2) 271 K - 
                   de Vries repulsive H}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293928},
  url          = {https://doi.org/10.5281/zenodo.1293928}
}

@misc{berger2POPEfiles,
  author       = {Thomas Piggot},
  title        = {{Berger POPE Simulations (versions 1 and 2) 303 K - 
                   larger repulsive H}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293891},
  url          = {https://doi.org/10.5281/zenodo.1293891}
}

@misc{bergerPOPEfiles,
  author       = {Thomas Piggot},
  title        = {{Berger POPE Simulations (versions 1 and 2) 303 K - 
                   de Vries repulsive H}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293889},
  url          = {https://doi.org/10.5281/zenodo.1293889}
}

@misc{OPLSuaPOPEfiles,
  author       = {Thomas Piggot},
  title        = {OPLS-UA POPE Simulations (versions 1 and 2) 303 K},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293855},
  url          = {https://doi.org/10.5281/zenodo.1293855}
}

@misc{OPLSuaWvdWPOPEfiles,
  author       = {Thomas Piggot},
  title        = {{OPLS-UA POPE Simulations (versions 1 and 2) 303 K 
                   with vdW on H atoms}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293853},
  url          = {https://doi.org/10.5281/zenodo.1293853}
}

@misc{charmm36uaPOPEfiles,
  author       = {Thomas Piggot},
  title        = {{CHARMM36-UA POPE Simulations (versions 1 and 2) 
                   310 K (NOTE: hexagonal membrane and POPE is called
                   PEUA)}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293774},
  url          = {https://doi.org/10.5281/zenodo.1293774}
}

@misc{gromos43a1s3POPEfiles,
  author       = {Thomas Piggot},
  title        = {{GROMOS 43A1-S3 POPE Simulations (versions 1 and 2) 
                   313 K (NOTE: anisotropic pressure coupling)}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293762},
  url          = {https://doi.org/10.5281/zenodo.1293762}
}

@article{dahlberg10,
author = {Dahlberg, Martin and Marini, Alberto and Mennucci, Benedetta and Maliniak, Arnold},
title = {Quantum Chemical Modeling of the Cardiolipin Headgroup},
journal = {The Journal of Physical Chemistry A},
volume = {114},
number = {12},
pages = {4375-4387},
year = {2010},
}

@article{zhao08,
title = "Role of phosphatidylglycerols in the stability of bacterial membranes",
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volume = "90",
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url = "http://www.sciencedirect.com/science/article/pii/S0300908408000692",
author = "Wei Zhao and Tomasz Róg and Andrey A. Gurtovenko and Ilpo Vattulainen and Mikko Karttunen",
}

@article{henin09,
author = {Hénin, Jérôme and Shinoda, Wataru and Klein, Michael L.},
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}

@article{pare98,
title = "Polymorphism of POPE/Cholesterol System: A 2H Nuclear Magnetic Resonance and Infrared Spectroscopic Investigation",
journal = "Biophysical Journal",
volume = "74",
number = "2",
pages = "899 - 909",
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issn = "0006-3495",
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author = "Chantal Paré and Michel Lafleur",
}

@misc{DOPC1DOPE1berger,
  author       = {Bacle, Am{\'e}lie and
                  Fuchs, Patrick F. J.},
  title        = {{Berger DOPC/DOPE (50:50 ratio) MD simulation (300 
                   K - 300ns - 1 bar)}},
  month        = aug,
  year         = 2018,
  doi          = {10.5281/zenodo.1402437},
  url          = {https://doi.org/10.5281/zenodo.1402437}
}

@misc{DOPCberger300K,
  author       = {Bacle, Am{\'e}lie and
                  Fuchs, Patrick F. J.},
  title        = {{Berger pure DOPC MD simulation (300 K - 300ns - 1 
                   bar)}},
  month        = aug,
  year         = 2018,
  doi          = {10.5281/zenodo.1402411},
  url          = {https://doi.org/10.5281/zenodo.1402411}
}

@misc{POPC1DOPE1berger,
  author       = {Bacle, Am{\'e}lie and
                  Fuchs, Patrick F. J.},
  title        = {{Berger POPC/DOPE (50:50 ratio) MD simulation (300 
                   K - 300ns - 1 bar)}},
  month        = aug,
  year         = 2018,
  doi          = {10.5281/zenodo.1402441},
  url          = {https://doi.org/10.5281/zenodo.1402441}
}

@misc{POPC1POPE1berger,
  author       = {Bacle, Am{\'e}lie and
                  Fuchs, Patrick F. J.},
  title        = {{Berger POPC/POPE (50:50 ratio) MD simulation (300 
                   K - 400ns - 1 bar)}},
  month        = aug,
  year         = 2018,
  doi          = {10.5281/zenodo.1402449},
  url          = {https://doi.org/10.5281/zenodo.1402449}
}

@misc{POPCberger300K,
  author       = {Bacle, Am{\'e}lie and
                  Fuchs, Patrick F. J.},
  title        = {{Berger pure POPC MD simulation (300 K - 300ns - 1 
                   bar)}},
  month        = aug,
  year         = 2018,
  doi          = {10.5281/zenodo.1402417},
  url          = {https://doi.org/10.5281/zenodo.1402417}
}

@misc{POPCcharmm300K,
  author       = {Papadopoulos, Chris and
                  Fuchs, Patrick F.J.},
  title        = {{CHARMM36 pure POPC MD simulation (300 K - 300ns - 
                   1 bar)}},
  month        = jul,
  year         = 2018,
  doi          = {10.5281/zenodo.1306800},
  url          = {https://doi.org/10.5281/zenodo.1306800}
}

@misc{POPC1POPE1charmm36,
  author       = {Papadopoulos, Chris and
                  Fuchs, Patrick F.J.},
  title        = {{CHARMM36 POPC/POPE (50\%-50\%) MD simulation (300 K - 300ns - 1 bar)}},
  month        = jul,
  year         = 2018,
  doi          = {10.5281/zenodo.1306821},
  url          = {https://doi.org/10.5281/zenodo.1306821}
}

@misc{POPC5POPS1noCaClCHARMM,
  author       = {Jesper J. Madsen},
  title        = {{MD simulations of bilayers containing PC/PS 
                   mixtures and CaCl\_2: 150POPC\_150POPS\_neutral}},
  month        = jan,
  year         = 2019,
  doi          = {10.5281/zenodo.2542164},
  url          = {https://doi.org/10.5281/zenodo.2542164}
}

@misc{POPC1POPS1noCaClCHARMM,
  author       = {Jesper J. Madsen},
  title        = {{MD simulations of bilayers containing PC/PS 
                   mixtures and CaCl\_2: 250POPC\_50POPS\_neutral}},
  month        = jan,
  year         = 2019,
  doi          = {10.5281/zenodo.2542151},
  url          = {https://doi.org/10.5281/zenodo.2542151}
}

@misc{POPC5POPS1with1MCaClCHARMM,
  author       = {Jesper J. Madsen},
  title        = {{MD simulations of bilayers containing PC/PS 
                   mixtures and CaCl\_2: 250POPC\_50POPS\_1MCaCl\_2}},
  month        = jan,
  year         = 2019,
  doi          = {10.5281/zenodo.2542135},
  url          = {https://doi.org/10.5281/zenodo.2542135}
}

@article{smith94,
   author = "Smith, David E. and Dang, Liem X.",
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   doi = "http://dx.doi.org/10.1063/1.466363" 
}

@article{dang06,
annote = {Dang ions - parameters},
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number = {47},
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pmid = {17125322},
publisher = {American Chemical Society},
title = {{Molecular simulation analysis and X-ray absorption measurement of Ca2+, K+ and Cl- ions in solution.}},
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volume = {110},
year = {2006}
}

@misc{POPC5POPS1withCaClCHARMM,
  author       = {Jesper J. Madsen},
  title        = {{MD simulations of bilayers containing PC/PS mixtures and CaCl\_2: 250POPC\_50POPS\_0.15MCaCl\_2}},
  month        = jan,
  year         = 2019,
  doi          = {10.5281/zenodo.2542176},
  url          = {https://doi.org/10.5281/zenodo.2542176}
}

@article{shirts07,
author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.},
title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations},
journal = {J. Phys. Chem. B},
volume = {111},
number = {45},
pages = {13052-13063},
year = {2007},
}


@article{rog16,
title = "Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters",
journal = "Data in Brief",
volume = "7",
pages = "1171 - 1174",
year = "2016",
issn = "2352-3409",
doi = "https://doi.org/10.1016/j.dib.2016.03.067",
url = "http://www.sciencedirect.com/science/article/pii/S2352340916301755",
author = "Tomasz R{\'o}g and Adam Orlowski and Alicia Llorente and Tore Skotland and Tuulia Sylv{\"a}nne and Dimple Kauhanen and Kim Ekroos and Kirsten Sandvig and Ilpo Vattulainen",
keywords = "Molecular dynamics simulations, Force field, Topology, Lipidomics, Lipid, GROMACS",
}

@article{kulig15c,
title = "Topologies, structures and parameter files for lipid simulations in GROMACS with the OPLS-aa force field: DPPC, POPC, DOPC, PEPC, and cholesterol",
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pages = "333 - 336",
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url = "http://www.sciencedirect.com/science/article/pii/S2352340915002073",
author = "Waldemar Kulig and Marta Pasenkiewicz-Gierula and Tomasz Róg",
}

@article{ghahremanpour13,
  title={MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program},
  author={Ghahremanpour, Mohammad Mehdi and Arab, Seyed Shahriar and Aghazadeh, Saman Biook and Zhang, Jin and van der Spoel, David},
  journal={Bioinformatics},
  volume={30},
  number={3},
  pages={439--441},
  year={2013},
  publisher={Oxford University Press}
}
 @article{jambeck2012another,
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  volume={9},
  number={1},
  pages={774--784},
  year={2012},
  publisher={ACS Publications}
}
 @article{abraham2015gromacs,
  title={GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers},
  author={Abraham, Mark James and Murtola, Teemu and Schulz, Roland and P{\'a}ll, Szil{\'a}rd and Smith, Jeremy C and Hess, Berk and Lindahl, Erik},
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  year={2015},
  publisher={Elsevier}
}


@misc{macrogPOPC298K,
  author       = {Javanainen, Matti},
  title        = {{Simulation of a POPC bilayer at 298K, lipid model 
                   by Maciejewski and Rog}},
  month        = feb,
  year         = 2018,
  doi          = {10.5281/zenodo.1167532},
  url          = {https://doi.org/10.5281/zenodo.1167532}
}

@misc{bergerPOPC310K,
  author       = {Ollila, O. H. Samuli},
  title        = {{MD simulation of POPC lipids bilayer at 310K 
                   (Berger, Gromacs 3.1.4)}},
  month        = apr,
  year         = 2018,
  doi          = {10.5281/zenodo.1230170},
  url          = {https://doi.org/10.5281/zenodo.1230170}
}

@article{lee16,
author = {Lee, Jumin and Cheng, Xi and Swails, Jason M. and Yeom, Min Sun and Eastman, Peter K. and Lemkul, Justin A. and Wei, Shuai and Buckner, Joshua and Jeong, Jong Cheol and Qi, Yifei and Jo, Sunhwan and Pande, Vijay S. and Case, David A. and Brooks, Charles L. and MacKerell, Alexander D. and Klauda, Jeffery B. and Im, Wonpil},
title = {CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field},
journal = {J. Chem. Theo. Comput.},
volume = {12},
number = {1},
pages = {405-413},
year = {2016},
}

@article{jo18,
author = {Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil},
title = {CHARMM-GUI: A web-based graphical user interface for CHARMM},
journal = {Journal of Computational Chemistry},
volume = {29},
number = {11},
pages = {1859-1865},
keywords = {molecular dynamics, Poisson-Boltzmann, electrostatic potential, membrane, visualization, explicit solvent, implicit solvent, MarvinSpace},
doi = {10.1002/jcc.20945},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20945},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20945},
}

@article{hallock18,
author = {Hallock, Michael
J. and Greenwood, Alexander I. and Wang, Yan and Morrissey, James H. and Tajkhorshid, Emad and Rienstra, Chad M. and Pogorelov, Taras V.},
title = {Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane},
journal = {Biochemistry},
volume = {57},
number = {50},
pages = {6897-6905},
year = {2018},
}

@misc{POPCslipids298K,
  author       = {Favela-Rosales, Fernando},
  title        = {{MD simulation trajectory of a lipid bilayer: Pure 
                   POPC in water. SLIPIDS, Gromacs 4.6.3. 2016.}},
  month        = nov,
  year         = 2016,
  doi          = {10.5281/zenodo.166034},
  url          = {https://doi.org/10.5281/zenodo.166034}
}

@misc{POPCcharmm36T303K,
  author       = {Melcr, Josef},
  title        = {{POPC lipid membrane, 303K, Charmm36 force field, 
                   simulation files and 200 ns trajectory for Gromacs
                   MD simulation engine v5.1.2}},
  month        = sep,
  year         = 2016,
  doi          = {10.5281/zenodo.153944},
  url          = {https://doi.org/10.5281/zenodo.153944}
}

@misc{buildHvalidation,
  author       = {Patrick Fuchs},
  title        = {Validation of buildH on a CHARMM36 POPC trajectory},
  month        = apr,
  year         = 2021,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.4715962},
  url          = {https://doi.org/10.5281/zenodo.4715962}
}

@software{buildH,
  author       = {Santuz, Hubert and
                  Bacle, Amélie and
                  Poulain, Pierre and
                  Fuchs, Patrick},
  title        = {{buildH (v1.2.0): Build hydrogens from a united- 
                   atom MD of lipids and calculate the order
                   parameter.}},
  month        = apr,
  year         = 2021,
  publisher    = {Zenodo},
  version      = {v1.2.0},
  doi          = {10.5281/zenodo.4676218},
  url          = {https://doi.org/10.5281/zenodo.4676218}
}


@misc{NMRlipidsIVbgit,
  author       = {O. H. Samuli Ollila and et al.},
  title       = {NMRLipidsIVb GitHub repository},
  doi          = {10.5281/zenodo.5118637},
  url          = {https://doi.org/10.5281/zenodo.5118637}
}

@misc{ECCpops,
  author       = {Melcr and et al.},
  title       = {ECCpops GitHub repository},
  url         = {https://github.com/jmelcr/ecc_lipids}
}

@misc{MATCHgit,
  author       = {O. H. Samuli Ollila and et al.},
  title       = {MATCH GitHub repository},
  url         = {https://github.com/NMRLipids/MATCH}
}

@article{agrawal11,
author = {Michaud-Agrawal, Naveen and Denning, Elizabeth J. and Woolf, Thomas B. and Beckstein, Oliver},
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volume = {32},
number = {10},
year = {2011},
pages = {2319-2327},
keywords = {molecular dynamics simulations, analysis, proteins, object-oriented design, software, membrane systems, Python programming language},
doi = {10.1002/jcc.21787},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21787},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.21787},
}

@InProceedings{gowers16,
  author    = { {R}ichard {J}. {G}owers and {M}ax {L}inke and {J}onathan {B}arnoud and {T}yler {J}. {E}. {R}eddy and {M}anuel {N}. {M}elo and {S}ean {L}. {S}eyler and {J}an {D}oma{\'n}ski and {D}avid {L}. {D}otson and {S}{\'e}bastien {B}uchoux and {I}an {M}. {K}enney and {O}liver {B}eckstein },
  title     = { {M}{D}{A}nalysis: {A} {P}ython {P}ackage for the {R}apid {A}nalysis of {M}olecular {D}ynamics {S}imulations },
  booktitle = { {P}roceedings of the 15th {P}ython in {S}cience {C}onference },
  pages     = { 98 - 105 },
  year      = { 2016 },
  editor    = { {S}ebastian {B}enthall and {S}cott {R}ostrup }
}

@article{valentine18,
title = "Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface",
journal = "Biophysical Journal",
volume = "115",
number = "8",
pages = "1541 - 1551",
year = "2018",
issn = "0006-3495",
doi = "https://doi.org/10.1016/j.bpj.2018.08.044",
url = "http://www.sciencedirect.com/science/article/pii/S0006349518310221",
author = "Mason L. Valentine and Alfredo E. Cardenas and Ron Elber and Carlos R. Baiz"}

@misc{charmm36pops+83popcT298Kwith890mMK,
  author       = {Ollila, O. H. S.},
  title        = {{POPC:POPS (5:1) with 890 mM potassium simulation 
                   with CHARMM36 at 298K}},
  month        = nov,
  year         = 2018,
  doi          = {10.5281/zenodo.1493246},
  url          = {https://doi.org/10.5281/zenodo.1493246}
}

@misc{charmm36pops+83popcT298Kwith450mMK,
  author       = {Ollila, O. H. S.},
  title        = {{POPC:POPS (5:1) with 450 mM potassium simulation 
                   with CHARMM36 at 298K}},
  month        = nov,
  year         = 2018,
  doi          = {10.5281/zenodo.1493241},
  url          = {https://doi.org/10.5281/zenodo.1493241}
}

@misc{charmm36pops+83popcT298Kwith890mMNa,
  author       = {Ollila, O. H. S.},
  title        = {{POPC:POPS (5:1) with 890 mM sodium simulation with 
                   CHARMM36 at 298K}},
  month        = nov,
  year         = 2018,
  doi          = {10.5281/zenodo.1493229},
  url          = {https://doi.org/10.5281/zenodo.1493229}
}

@misc{charmm36pops+83popcT298Kwith440mMNa,
  author       = {Ollila, O. H. S.},
  title        = {{POPC:POPS (5:1) with 440 mM sodium simulation with 
                   CHARMM36 at 298K}},
  month        = nov,
  year         = 2018,
  doi          = {10.5281/zenodo.1493190},
  url          = {https://doi.org/10.5281/zenodo.1493190}
}

@misc{bergerPOPSPOPC4:1mixtureT310K,
  author       = {Ollila O. H. Samuli},
  title        = {{POPC:POPS (4:1) simulation with Berger model at 
                   310K}},
  month        = oct,
  year         = 2018,
  doi          = {10.5281/zenodo.1475285},
  url          = {https://doi.org/10.5281/zenodo.1475285}
}

@misc{macrogPOPS298KwithK,
  author       = {Javanainen, Matti},
  title        = {{Simulation of a POPS membrane with potassium 
                   counterions}},
  month        = sep,
  year         = 2018,
  doi          = {10.5281/zenodo.1434990},
  url          = {https://doi.org/10.5281/zenodo.1434990}
}

@article{petrache04,
title = "Structure and Fluctuations of Charged Phosphatidylserine Bilayers in the Absence of Salt",
journal = "Biophysical Journal",
volume = "86",
number = "3",
pages = "1574 - 1586",
year = "2004",
author = "Horia I. Petrache and Stephanie Tristram-Nagle and Klaus Gawrisch and Daniel Harries and V. Adrian Parsegian and John F. Nagle"
}

@misc{slipidsPOPEfiles,
  author       = {Thomas Piggot},
  title        = {{Slipids POPE Simulations (versions 1 and 2) 310 K 
                   (NOTE: hexagonal membrane)}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1293813},
  url          = {https://doi.org/10.5281/zenodo.1293813}
}

@article{bak00,
title = "SIMPSON: A General Simulation Program for Solid-State NMR Spectroscopy",
journal = "J. Magn. Reson.",
volume = "147",
number = "2",
pages = "296 - 330",
year = "2000",
issn = "1090-7807",
doi = "https://doi.org/10.1006/jmre.2000.2179",
url = "http://www.sciencedirect.com/science/article/pii/S1090780700921797",
author = "Mads Bak and Jimmy T Rasmussen and Niels Chr Nielsen"
}

@misc{charmmPOPC450mMCaClfiles,
  author       = {Javanainen, Matti},
  title        = {{POPC @ 310K, 450 mM of CaCl\_2. Charmm36 with default Charmm ions}},
  month        = may,
  year         = 2016,
  doi          = {10.5281/zenodo.51185},
  url          = {http://dx.doi.org/10.5281/zenodo.51185}
}

@misc{nencineCHARMM36popcT310K,
  author       = {Nencini, Ricky},
  title        = {{Simulation data for CHARMM36 POPC bilayer, 100 
                   lipids/leaflet, 310K, GROMACS 5.1.4}},
  month        = mar,
  year         = 2018,
  doi          = {10.5281/zenodo.1198158},
  url          = {https://doi.org/10.5281/zenodo.1198158}
}

@misc{CHARMM36withNaClNBfix,
  author       = {Nencini, Ricky},
  title        = {{Simulation data for CHARMM36 POPC bilayer, 100 
                   lipids/leaflet, 940 mM NaCl, 310K, GROMACS 5.1.4}},
  month        = mar,
  year         = 2018,
  doi          = {10.5281/zenodo.1198454},
  url          = {https://doi.org/10.5281/zenodo.1198454}
}

@article{millman82,
title = "Effects of monovalent ion binding and screening on measured electrostatic forces between charged phospholipid bilayers",
journal = "Biophysical Journal",
volume = "40",
number = "3",
pages = "221 - 232",
year = "1982",
author = "M.E. Loosley-Millman and R.P. Rand and V.A. Parsegian"
}

@article{rand89,
title = "Hydration forces between phospholipid bilayers",
journal = "Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes",
volume = "988",
number = "3",
pages = "351 - 376",
year = "1989",
author = "R.P. Rand and V.A. Parsegian"
}

@article{roux88,
author="Roux, M.
and Neumann, J.-M.
and Bloom, M.
and Devaux, P. F.",
title="2H and 31P NMR study of pentalysine interaction with headgroup deuterated phosphatidylcholine and phosphatidylserine",
journal="European Biophysics Journal",
year="1988",
month="Dec",
day="01",
volume="16",
number="5",
pages="267--273",
}

@misc{CHARMM36withCaClNBfix,
  author       = {Nencini, Ricky},
  title        = {{Simulation data for CHARMM36 POPC bilayer, 100 
                   lipids/leaflet, 450 mM CaCl2 ("NB-Fix" used),
                   310K, GROMACS 5.1.4}},
  month        = mar,
  year         = 2018,
  doi          = {10.5281/zenodo.1198171},
  url          = {https://doi.org/10.5281/zenodo.1198171}
}

@misc{CHARMM36cationicSURF,
  author       = {Ollila, O. H. Samuli},
  title        = {{CHARMM36 simulations of POPC mixed with cationic 
                   surfactant}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1288297},
  url          = {https://doi.org/10.5281/zenodo.1288297}
}

@misc{POPCpopsGROMOSCKPMwithNa,
  author       = {Thomas Piggot},
  title        = {{GROMOS-CKP POPS/POPC simulations (versions 1 and 
                   2) 298 K with Berger/Chiu NH3 charges and PME}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1283331},
  url          = {https://doi.org/10.5281/zenodo.1283331}
}

@misc{POPCpopsGROMOSCKPwithNa,
  author       = {Thomas Piggot},
  title        = {{GROMOS-CKP POPS/POPC simulations (versions 1 and 
                   2) 298 K with GROMOS NH3 charges and PME}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1283333},
  url          = {https://doi.org/10.5281/zenodo.1283333}
}

@misc{POPCpopsLIPID17withCaCl,
  author       = {Batuhan Kav and
                  Markus S. Miettinen},
  title        = {{Amber Lipid17 Simulations of POPC/POPS Membranes 
                   with CaCl2}},
  month        = jul,
  year         = 2018,
  note         = {{B.K acknowledges financial support from 
                   International Max Planck Research School on
                   Multiscale Bio-Systems}},
  doi          = {10.5281/zenodo.1438848},
  url          = {https://doi.org/10.5281/zenodo.1438848}
}

@misc{POPCpopsLIPID17withKCI,
  author       = {Kav, Batuhan and
                  Miettinen, Markus S.},
  title        = {{Amber Lipid17 Simulations of POPC/POPS Membranes 
                   with KCl Counterions}},
  month        = may,
  year         = 2018,
  note         = {{B.K acknowledges financial support from 
                   International Max Planck Research School on
                   Multiscale Bio-Systems}},
  doi          = {10.5281/zenodo.1250969},
  url          = {https://doi.org/10.5281/zenodo.1250969}
}

@misc{POPCpopsLIPID17withNaCI,
  author       = {Kav, Batuhan and
                  Miettinen, Markus S.},
  title        = {{Amber Lipid17 Simulations of POPC/POPS Membranes 
                   with NaCl Counterions}},
  month        = may,
  year         = 2018,
  note         = {{B.K acknowledges financial support from 
                   International Max Planck Research School on
                   Multiscale Bio-Systems}},
  doi          = {10.5281/zenodo.1250975},
  url          = {https://doi.org/10.5281/zenodo.1250975}
}

@misc{POPCpopsLIPID17withNa,
  author       = {Kav, Batuhan and
                  Miettinen, Markus S.},
  title        = {{Amber Lipid17 Simulations of POPC/POPS Membranes 
                   with NaCl}},
  month        = apr,
  year         = 2018,
  note         = {{B.K acknowledges financial support from 
                   International Max Planck Research School on
                   Multiscale Bio-Systems}},
  doi          = {10.5281/zenodo.1227272},
  url          = {https://doi.org/10.5281/zenodo.1227272}
}

@misc{POPCpopsBERGERwith715mMCa,
  author       = {Cwiklik Lukasz},
  title        = {{MD simulation trajectory of a POPC/POPS (4:1) 
                   bilayer with 715mM CaCl2, Berger force field for
                   lipids, scaled charges for Ca2+ and Cl-}},
  month        = sep,
  year         = 2017,
  doi          = {10.5281/zenodo.887400},
  url          = {https://doi.org/10.5281/zenodo.887400}
}

@misc{POPCpopsBERGERwith102mMCa,
  author       = {Cwiklik Lukasz},
  title        = {{MD simulation trajectory of a POPC/POPS (4:1) 
                   bilayer with 102mM CaCl2, Berger force field for
                   lipids, scaled charges for Ca2+ and Cl-}},
  month        = sep,
  year         = 2017,
  doi          = {10.5281/zenodo.887398},
  url          = {https://doi.org/10.5281/zenodo.887398}
}

@misc{POPCpopsBERGERwith1000mMNa,
  author       = {Cwiklik, Lukasz},
  title        = {{MD simulation trajectory of a POPC/POPS (4:1) 
                   bilayer with 1M NaCl, Berger force field for
                   lipids and ffgmx for ions}},
  month        = aug,
  year         = 2017,
  doi          = {10.5281/zenodo.838219},
  url          = {https://doi.org/10.5281/zenodo.838219}
}

@misc{POPCpopsLIPID17withK,
  author       = {Kav, Batuhan and
                  Miettinen, Markus S.},
  title        = {{Amber Lipid17 Simulations of POPC/POPS Membranes 
                   with KCl}},
  month        = apr,
  year         = 2018,
  note         = {{B.K acknowledges financial support from 
                   International Max Planck Research School on
                   Multiscale Bio-Systems}},
  doi          = {10.5281/zenodo.1227257},
  url          = {https://doi.org/10.5281/zenodo.1227257}
}

@misc{POPCpopsMACROGwithK,
  author       = {Javanainen, Matti},
  title        = {Simulations of POPC/POPS membranes with KCl},
  month        = mar,
  year         = 2018,
  doi          = {10.5281/zenodo.1404040},
  url          = {https://doi.org/10.5281/zenodo.1404040}
}

@article{jurkiewicz12,
title = "Structure, dynamics, and hydration of POPC/POPS bilayers suspended in NaCl, KCl, and CsCl solutions",
journal = "Biochimica et Biophysica Acta (BBA) - Biomembranes",
volume = "1818",
number = "3",
pages = "609 - 616",
year = "2012",
author = "Piotr Jurkiewicz and Lukasz Cwiklik and Alžběta Vojtíšková and Pavel Jungwirth and Martin Hof",
}

@article{vangaveti14,
author = {Vangaveti,S.  and Travesset,A. },
title = {Separation of the Stern and diffuse layer in coarse-grained models: The cases of phosphatidyl serine, phosphatidic acid, and PIP2 monolayers},
journal = {The Journal of Chemical Physics},
volume = {141},
number = {24},
pages = {245102},
year = {2014},
}

@article{molina12,
title = "Effect of Calcium and Magnesium on Phosphatidylserine Membranes: Experiments and All-Atomic Simulations",
journal = "Biophysical Journal",
volume = "102",
number = "9",
pages = "2095 - 2103",
year = "2012",
author = "Alberto Martín-Molina and César Rodríguez-Beas and Jordi Faraudo"
}

@article{eisenberg79,
author = {Eisenberg, Moises and Gresalfi, Thomas and Riccio, Thomas and McLaughlin, Stuart},
title = {Adsorption of monovalent cations to bilayer membranes containing negative phospholipids},
journal = {Biochemistry},
volume = {18},
number = {23},
pages = {5213-5223},
year = {1979},
}

@article{dluhy83,
author = {Dluhy, Richard and Cameron, David G. and Mantsch, Henry H. and Mendelsohn, Richard},
title = {Fourier transform infrared spectroscopic studies of the effect of calcium ions on phosphatidylserine},
journal = {Biochemistry},
volume = {22},
number = {26},
pages = {6318-6325},
year = {1983},
}

@article{cascales96,
author = {López Cascales,J. J.  and García de la Torre,J.  and Marrink,S. J.  and Berendsen,H. J. C. },
title = {Molecular dynamics simulation of a charged biological membrane},
journal = {The Journal of Chemical Physics},
volume = {104},
number = {7},
pages = {2713-2720},
year = {1996},
}


@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 = {J. Phys.Chem. B},
volume = {122},
number = {16},
pages = {4546-4557},
year = {2018},
}

@article{venable13,
author = {Venable, Richard M. and Luo, Yun and Gawrisch, Klaus and Roux, Benoît and Pastor, Richard W.},
title = {Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data},
journal = {J. Phys. Chem. B},
volume = {117},
number = {35},
pages = {10183-10192},
year = {2013},
}

@article{mattai89,
author = {Mattai, Jairajh and Hauser, Helmut and Demel, Rudy A. and Shipley, G. Graham},
title = {Interactions of metal ions with phosphatidylserine bilayer membranes: effect of hydrocarbon chain unsaturation},
journal = {Biochemistry},
volume = {28},
number = {5},
pages = {2322-2330},
year = {1989},
}

@article{hauser83,
author = {Hauser, Helmut and Shipley, G. Graham},
title = {Interactions of monovalent cations with phosphatidylserine bilayer membranes},
journal = {Biochemistry},
volume = {22},
number = {9},
pages = {2171-2178},
year = {1983},
}

@article{feigenson86,
author = {Feigenson, G. W.},
title = {On the nature of calcium ion binding between phosphatidylserine lamellae},
journal = {Biochemistry},
volume = {25},
number = {19},
pages = {5819-5825},
year = {1986},
}

@article{hauser85,
title = "Comparative structural aspects of cation binding to phosphatidylserine bilayers",
journal = "Biochimica et Biophysica Acta (BBA) - Biomembranes",
volume = "813",
number = "2",
pages = "343 - 346",
year = "1985",
issn = "0005-2736",
doi = "https://doi.org/10.1016/0005-2736(85)90251-2",
url = "http://www.sciencedirect.com/science/article/pii/0005273685902512",
author = "Helmut Hauser and G.Graham Shipley",
keywords = "Phosphatidylserine bilayer, Phospholipid-cation complex, Membrane structure, X-ray diffraction"
}

@article{hauser84,
author = {Hauser, Helmut and Shipley, G. Graham},
title = {Interactions of divalent cations with phosphatidylserine bilayer membranes},
journal = {Biochemistry},
volume = {23},
number = {1},
pages = {34-41},
year = {1984},
}


@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",
volume = "88",
number = "3",
pages = "927 - 932",
year = "1979",
issn = "0006-291X",
doi = "https://doi.org/10.1016/0006-291X(79)91497-9",
url = "http://www.sciencedirect.com/science/article/pii/0006291X79914979",
author = "Robert J. Kurland"
}

@article{hauser77,
title = "Crystalline anhydrous Ca-phosphatidylserine bilayers",
journal = "Biochemical and Biophysical Research Communications",
volume = "76",
number = "2",
pages = "267 - 274",
year = "1977",
issn = "0006-291X",
doi = "https://doi.org/10.1016/0006-291X(77)90721-5",
url = "http://www.sciencedirect.com/science/article/pii/0006291X77907215",
author = "H. Hauser and E.G. Finer and A. Darke"
}

@misc{charmm36pops+83popcT298KpiggotSODIUM,
  author       = {Thomas Piggot},
  title        = {{CHARMM36 POPS/POPC simulations (versions 1 and 2) 
                   298 K 1.0 nm LJ switching with Na ions}},
  month        = feb,
  year         = 2018,
  doi          = {10.5281/zenodo.1182665},
  url          = {https://doi.org/10.5281/zenodo.1182665}
}

@misc{charmm36pops+83popcT298Kpiggot,
  author       = {Thomas Piggot},
  title        = {{CHARMM36 POPS/POPC simulations (versions 1 and 2) 
                   298 K 1.0 nm LJ switching with K ions}},
  month        = feb,
  year         = 2018,
  doi          = {10.5281/zenodo.1182658},
  url          = {https://doi.org/10.5281/zenodo.1182658}
}

@article{kim16,
title = "Bilayer Properties of Lipid A from Various Gram-Negative Bacteria",
journal = "Biophysical Journal",
volume = "111",
number = "8",
pages = "1750 - 1760",
year = "2016",
issn = "0006-3495",
doi = "https://doi.org/10.1016/j.bpj.2016.09.001",
url = "http://www.sciencedirect.com/science/article/pii/S0006349516307615",
author = "Seonghoon Kim and Dhilon S. Patel and Soohyung Park and Joanna Slusky and Jeffery B. Klauda and Göran Widmalm and Wonpil Im"
}

@misc{POPCpopsMACROG,
  author       = {Javanainen, Matti},
  title        = {Simulations of POPC/POPS membranes with CaCl\_2.},
  month        = sep,
  year         = 2017,
  doi          = {10.5281/zenodo.1409551},
  url          = {https://doi.org/10.5281/zenodo.1409551}
}


@misc{lipid17_nacl_kcl_series,
  author       = {Melcr, Josef},
  title        = {{Molecular dynamics simulations of lipid bilayers 
                   containing POPC and POPS with the lipid17 force
                   field, NaCl and KCl salt concentrations}},
  month        = nov,
  year         = 2018,
  doi          = {10.5281/zenodo.1487895},
  url          = {https://doi.org/10.5281/zenodo.1487895}
}

@misc{lipid17_ff99_ions,
  author       = {Melcr, Josef},
  title        = {{Molecular dynamics simulations of lipid bilayers 
                   containing POPC and POPS with the lipid17 force
                   field and ff99 ions}},
  month        = nov,
  year         = 2018,
  doi          = {10.5281/zenodo.1487906},
  url          = {https://doi.org/10.5281/zenodo.1487906}
}

@misc{lipid17_cacl_series,
  author       = {Melcr, Josef},
  title        = {{Molecular dynamics simulations of lipid bilayers 
                   containing POPC and POPS with the lipid17 force
                   field, only counterions, and CaCl2 concentrations}},
  month        = nov,
  year         = 2018,
  doi          = {10.5281/zenodo.1487761},
  url          = {https://doi.org/10.5281/zenodo.1487761}
}


@misc{lipid17POPSjcions,
  author       = {Miettinen, Markus S. and
                  Kav, Batuhan},
  title        = {{Molecular dynamics simulation trajectory of an 
                   anionic lipid bilayer: 100 mol\% POPS with Na+
                   counterions using Joung-Cheatham Ions}},
  month        = jan,
  year         = 2018,
  note         = {{B.K. acknowledges financial support from 
                   International Max Planck Research School on
                   Multiscale Bio-Systems.}},
  doi          = {10.5281/zenodo.1148495},
  url          = {https://doi.org/10.5281/zenodo.1148495}
}

@misc{lipid17POPSff99ions,
  author       = {Miettinen, Markus S. and
                  Kav, Batuhan},
  title        = {{Molecular dynamics simulation trajectory of an 
                   anionic lipid bilayer: 100 mol\% POPS with Na+
                   counterions using ff99 ions}},
  month        = jan,
  year         = 2018,
  note         = {{B.K. acknowledges financial support from 
                   International Max Planck Research School on
                   Multiscale Bio-Systems}},
  doi          = {10.5281/zenodo.1134869},
  url          = {https://doi.org/10.5281/zenodo.1134869}
}

@article{joung08,
author = {Joung, In Suk and Cheatham, Thomas E.},
title = {Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations},
journal = {The Journal of Physical Chemistry B},
volume = {112},
number = {30},
pages = {9020-9041},
year = {2008},
}

@article{aqvist90,
author = { Johan.  \r{A}qvist },
title = {Ion-water interaction potentials derived from free energy perturbation simulations},
journal = {J. Phys. Chem.},
volume = {94},
number = {21},
pages = {8021-8024},
year = {1990},
}

@misc{lipid17DOPSff99ions,
  author       = {Kav, Batuhan and
                  Miettinen, Markus S.},
  title        = {{Molecular dynamics simulation trajectory of an 
                   anionic lipid bilayer: 100 mol\% DOPS with Na+
                   counterions using ff99 Ions}},
  month        = jan,
  year         = 2018,
  note         = {{B.K acknowledges financial support from 
                   International Max Planck Research School on
                   Multiscale Bio-Systems}},
  doi          = {10.5281/zenodo.1135142},
  url          = {https://doi.org/10.5281/zenodo.1135142}
}

@misc{lipid17DOPSjcions,
  author       = {Kav, Batuhan and
                  Miettinen, Markus S.},
  title        = {{Molecular dynamics simulation trajectory of an 
                   anionic lipid bilayer: 100 mol\% DOPS with Na+
                   counterions using Joung-Cheetham Ions}},
  month        = jan,
  year         = 2018,
  note         = {{B.K acknowledges financial support from 
                   International Max Planck Research School on
                   Multiscale Bio-Systems}},
  doi          = {10.5281/zenodo.1134871},
  url          = {https://doi.org/10.5281/zenodo.1134871}
}

@misc{gould18,
author = "Gould, I.R. and Skjevik, A.A. and Dickson, C.J. and Madej, B.D. and Walker, R.C.",
title = "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids",
year = "2018",
note = "In preparation"
}

@article{pedersen06,
title = "The effect of calcium on the properties of charged phospholipid bilayers",
journal = "Biochimica et Biophysica Acta (BBA) - Biomembranes",
volume = "1758",
number = "5",
pages = "573 - 582",
year = "2006",
author = "Ulf R. Pedersen and Chad Leidy and Peter Westh and Günther H. Peters",
keywords = "Molecular dynamics simulation, Fluorescence spectroscopy, DMPG, DMPS, Lipid order, Ion distribution, Membranes"
}

@article{pandit02,
title = "Molecular Dynamics Simulation of Dipalmitoylphosphatidylserine Bilayer with Na+ Counterions",
journal = "Biophysical Journal",
volume = "82",
number = "4",
pages = "1818 - 1827",
year = "2002",
author = "Sagar A. Pandit and Max L. Berkowitz"
}

@article{roux86,
author = {Roux, Michel and Neumann, Jean-Michel},
title = {Deuterium NMR study of head-group deuterated phosphatidylserine in pure and binary phospholipid bilayers},
journal = {FEBS Letters},
volume = {199},
number = {1},
pages = {33--38},
year = {1986},
}


@article{boettcher11,
author = {Boettcher, John M. and Davis-Harrison, Rebecca L. and Clay, Mary C. and Nieuwkoop, Andrew J. and Ohkubo, Y. Zenmei and Tajkhorshid, Emad and Morrissey, James H. and Rienstra, Chad M.},
title = {Atomic View of Calcium-Induced Clustering of Phosphatidylserine in Mixed Lipid Bilayers},
journal = {Biochemistry},
volume = {50},
number = {12},
pages = {2264-2273},
year = {2011},
}


@article{vernier09,
author = {Vernier, P. Thomas and Ziegler, Matthew J. and Dimova, Rumiana},
title = {Calcium Binding and Head Group Dipole Angle in Phosphatidylserine−Phosphatidylcholine Bilayers},
journal = {Langmuir},
volume = {25},
number = {2},
pages = {1020-1027},
year = {2009},
}

@article{sinn06,
title = "Binding of calcium to phosphatidylcholine–phosphatidylserine membranes",
journal = "Colloids and Surfaces A: Physicochemical and Engineering Aspects",
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"
}

@article{zhao04,
author = {Zhao, Hongxia and Tuominen, Esa K. J. and Kinnunen, Paavo K. J.},
title = {Formation of Amyloid Fibers Triggered by Phosphatidylserine-Containing Membranes},
journal = {Biochemistry},
volume = {43},
number = {32},
pages = {10302-10307},
year = {2004},
}


@article{gorbenko06,
title = "The role of lipid–protein interactions in amyloid-type protein fibril formation",
journal = "Chemistry and Physics of Lipids",
volume = "141",
number = "1",
pages = "72 - 82",
year = "2006",
author = "Galyna P. Gorbenko and Paavo K.J. Kinnunen",
keywords = "Protein–lipid interactions, Membrane-induced protein aggregation, Amyloid fibrils"
}

@misc{charmm36POPS298Kpotassium,
  author       = {Thomas Piggot},
  title        = {{CHARMM36 POPS simulations (versions 1 and 2) 298 K 
                   1.0 nm LJ switching with K ions}},
  month        = feb,
  year         = 2018,
  doi          = {10.5281/zenodo.1182654},
  url          = {https://doi.org/10.5281/zenodo.1182654}
}

@article{melcrova16,
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@misc{ckp2POPS303K,
  author       = {Thomas Piggot},
  title        = {{GROMOS-CKP POPS simulations (versions 1 and 2) 298 
                   K with GROMOS NH3 charges and PME}},
  month        = dec,
  year         = 2017,
  doi          = {10.5281/zenodo.1129435},
  url          = {https://doi.org/10.5281/zenodo.1129435}
}

@misc{ckp1POPS303K,
  author       = {Thomas Piggot},
  title        = {{GROMOS-CKP POPS simulations (versions 1 and 2) 298 
                   K with Berger/Chiu NH3 charges and PME}},
  month        = dec,
  year         = 2017,
  doi          = {10.5281/zenodo.1129431},
  url          = {https://doi.org/10.5281/zenodo.1129431}
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@misc{ckp2DOPS303K,
  author       = {Thomas Piggot},
  title        = {{GROMOS-CKP DOPS simulations (versions 1 and 2) 303 
                   K with GROMOS NH3 charges and PME}},
  month        = dec,
  year         = 2017,
  doi          = {10.5281/zenodo.1129447},
  url          = {https://doi.org/10.5281/zenodo.1129447}
}

@misc{ckp1DOPS303K,
  author       = {Thomas Piggot},
  title        = {{GROMOS-CKP DOPS simulations (versions 1 and 2) 303 
                   K with Berger/Chiu NH3 charges and PME}},
  month        = dec,
  year         = 2017,
  doi          = {10.5281/zenodo.1129429},
  url          = {https://doi.org/10.5281/zenodo.1129429}
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@misc{macrogPOPS298Kcorrect,
  author       = {Thomas Piggot},
  title        = {{MacRog POPS simulations (versions 1 and 2) 298 K 
                   with corrected PO not OP tails}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.1283335},
  url          = {https://doi.org/10.5281/zenodo.1283335}
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@misc{macrogPOPS298K,
  author       = {Javanainen, Matti},
  title        = {Simulation of a POPS bilayer},
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  url          = {https://doi.org/10.5281/zenodo.1120287}
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@misc{bergerPOPS298K,
  author       = {Thomas Piggot},
  title        = {{Berger POPS simulations (versions 1 and 2) 298 K 
                   1.0 nm cut-off}},
  month        = dec,
  year         = 2017,
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  url          = {https://doi.org/10.5281/zenodo.1129425}
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@misc{slipidsPOPS298K,
  author       = {Thomas Piggot},
  title        = {{Slipids POPS simulations (versions 1 and 2) 298 K 
                   1.0 nm cut-off with LJ-PME}},
  month        = dec,
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  url          = {https://doi.org/10.5281/zenodo.1129441}
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@misc{charmm36uaPOPS298K,
  author       = {Thomas Piggot},
  title        = {{CHARMM36-UA POPS simulations (versions 1 and 2) 
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@misc{charmm36POPS298K,
  author       = {Thomas Piggot},
  title        = {{CHARMM36 POPS simulations (versions 1 and 2) 298 K 
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  doi          = {10.5281/zenodo.1129415},
  url          = {https://doi.org/10.5281/zenodo.1129415}
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@misc{bergerDOPS303K,
  author       = {Thomas Piggot},
  title        = {{Berger DOPS simulations (versions 1 and 2) 303 K 
                   1.0 nm cut-off}},
  month        = dec,
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  doi          = {10.5281/zenodo.1129419},
  url          = {https://doi.org/10.5281/zenodo.1129419}
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@misc{slipidsDOPS303K,
  author       = {Thomas Piggot},
  title        = {{Slipids DOPS simulations (versions 1 and 2) 303 K 
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  month        = dec,
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  doi          = {10.5281/zenodo.1129439},
  url          = {https://doi.org/10.5281/zenodo.1129439}
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@misc{charmm36uaDOPS303K,
  author       = {Thomas Piggot},
  title        = {{CHARMM36-UA DOPS simulations (versions 1 and 2) 
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@misc{charmm36DOPS303K,
  author       = {Thomas Piggot},
  title        = {{CHARMM36 DOPS simulations (versions 1 and 2) 303 K 
                   1.0 nm LJ switching}},
  month        = dec,
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  doi          = {10.5281/zenodo.1129411},
  url          = {https://doi.org/10.5281/zenodo.1129411}
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@misc{charmm36pops+83popcT298K,
  author       = {Ollila, O. H. Samuli},
  title        = {{POPS+83\%popc lipid bilayer simulation at T298K ran CHARMM\_GUI force field and Gromacs}},
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  doi          = {10.5281/zenodo.1011104},
  url          = {https://doi.org/10.5281/zenodo.1011104}
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@misc{slipidsDPPGfilesT298K,
  author       = {Favela-Rosales, Fernando},
  title        = {{MD simulation trajectory of a fully hydrated DPPG 
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@misc{slipidsDPPGfiles,
  author       = {Favela-Rosales, Fernando},
  title        = {{MD simulation trajectory of a fully hydrated DPPG 
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@misc{slipidsPOPGfiles,
  author       = {Favela-Rosales, Fernando},
  title        = {{MD simulation trajectory of a fully hydrated POPG 
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@misc{slipidsDOPSfiles,
  author       = {Favela-Rosales, Fernando},
  title        = {{MD simulation trajectory of a fully hydrated DOPS 
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@misc{signPOST,
  title        = {The NMRLipids project, On the signs of the order parameters},
  year         = 2014,
  url          = {http://web.archive.org/web/20150414085027/http://nmrlipids.blogspot.fi/2014/04/on-signs-of-order-parameters.html}
}

@misc{accuracyPOST,
  title        = {The NMRLipids project, Accuracy of order parameter measurements },
  year         = 2014,
  url          = {http://web.archive.org/web/20150414085355/http://nmrlipids.blogspot.fi/2014/02/accuracy-of-order-parameter-measurements.html}
}

@misc{creditsPOST,
  title        = {The NMRLipids project, On creadits},
  year         = 2013,
  url          = {http://web.archive.org/web/20150414092532/http://nmrlipids.blogspot.fi/2013/07/on-credits.html}
}

@misc{nmrlipids,
  title        = {The NMRLipids project},
  year         = 2015,
  url          = {http://web.archive.org/web/20150414084452/http://nmrlipids.blogspot.fi}
}


@misc{charmmUAfilesLEE,
  author       = {Loison, Claire},
  title        = {{Hydrated DPPC, {MD} simulation trajectory and 
                   related files for UA charmm36 model by Lee et al
                   2014}},
  month        = apr,
  year         = 2015,
  doi          = {10.5281/zenodo.17004},
  url          = {http://dx.doi.org/10.5281/zenodo.17004}
}

@article{phillips05,
author = {Phillips, James C and Braun, Rosemary and Wang, Wei and Gumbart, James and Tajkhorshid, Emad and Villa, Elizabeth and Chipot, Christophe and Skeel, Robert D and Kal{\'e}, Laxmikant and Schulten, Klaus},
title = {{Scalable molecular dynamics with NAMD}},
journal = {J. Comput. Chem.},
year = {2005},
volume = {26},
number = {16},
pages = {1781--1802}
}

@misc{charmmPOPC512files,
  author       = {Favela-Rosales Fernando},
  title        = {POPC\_Glycerol\_CHARMM36\_0-10-15-20-25-35-50\%CHOL},
  month        = apr,
  year         = 2015,
  note         = {{Because of the system size, the files ONLY contain 
                   the coordinates of Glycerol saved every 10ps, this
                   is the real contribution to the nmrlipids project.}},
  doi          = {10.5281/zenodo.16830},
  url          = {http://dx.doi.org/10.5281/zenodo.16830}
}

@article{Lyubartsev00,
title = "M.DynaMix – a scalable portable parallel \{MD\} simulation package for arbitrary molecular mixtures ",
journal = "Comp. Phys. Comm.",
volume = "128",
number = "3",
pages = "565 - 589",
year = "2000",
author = "Alexander P. Lyubartsev and Aatto Laaksonen",
}

@misc{hogbergDMPCfiles,
  author       = {Alexander Lyubartsev},
  title        = {{{MD} simulation trajectory and related files for 
                   DMPC bilayer, H{\"o}gberg et al, J.Comp.Chem., 29,
                   2359 (2008)}},
  month        = mar,
  year         = 2015,
  doi          = {10.5281/zenodo.16195},
  url          = {http://dx.doi.org/10.5281/zenodo.16195}
}

@misc{hogbergPOPCfiles,
  author       = {Alexander Lyubartsev},
  title        = {{{MD} simulation trajectory and related files for 
                   POPC bilayer, H{\"o}gberg et al parameters
                   (J.Comp.Chem., 29, 2359 (2008))}},
  month        = apr,
  year         = 2015,
  doi          = {10.5281/zenodo.16724},
  url          = {http://dx.doi.org/10.5281/zenodo.16724}
}

@article{kanduc13,
author = {Kanduc, Matej and Schneck, Emanuel and Netz, Roland R.},
title = {Hydration Interaction between Phospholipid Membranes: Insight into Different Measurement Ensembles from Atomistic Molecular Dynamics Simulations},
journal = {Langmuir},
volume = {29},
number = {29},
pages = {9126-9137},
year = {2013},
}

@misc{bergerFILESdlpc4,
  author       = {Matej Kanduc},
  title        = {{{MD} trajectory for DLPC bilayer (Berger, Gromacs 4.5.4), nw=4 w/l}},
  month        = mar,
  year         = 2015,
  doi          = {10.5281/zenodo.16295},
  url          = {http://dx.doi.org/10.5281/zenodo.16295}
}

@misc{bergerFILESdlpc8,
  author       = {Matej Kanduc},
  title        = {{{MD} trajectory for DLPC bilayer (Berger, Gromacs 
                   4.5.4), nw=8 w/l}},
  month        = mar,
  year         = 2015,
  doi          = {10.5281/zenodo.16294},
  url          = {http://dx.doi.org/10.5281/zenodo.16294}
}

@misc{bergerFILESdlpc12,
  author       = {Matej Kanduc},
  title        = {{{MD} trajectory for DLPC bilayer (Berger, Gromacs 
                   4.5.4), nw=28 w/l}},
  month        = mar,
  year         = 2015,
  doi          = {10.5281/zenodo.16293},
  url          = {http://dx.doi.org/10.5281/zenodo.16293}
}

@misc{bergerFILESdlpc16,
  author       = {Matej Kanduc},
  title        = {{{MD} trajectory for DLPC bilayer (Berger, Gromacs 
                   4.5.4), nw=16 w/l}},
  month        = mar,
  year         = 2015,
  doi          = {10.5281/zenodo.16292},
  url          = {http://dx.doi.org/10.5281/zenodo.16292}
}

@misc{bergerFILESdlpc20,
  author       = {Matej Kanduc},
  title        = {{{MD} trajectory for DLPC bilayer (Berger, Gromacs 
                   4.5.4), nw=20 w/l}},
  month        = mar,
  year         = 2015,
  doi          = {10.5281/zenodo.16291},
  url          = {http://dx.doi.org/10.5281/zenodo.16291}
}

@misc{bergerFILESdlpc24,
  author       = {Matej Kanduc},
  title        = {{{MD} trajectory for DLPC bilayer (Berger, Gromacs 
                   4.5.4), nw=24 w/l}},
  month        = mar,
  year         = 2015,
  doi          = {10.5281/zenodo.16289},
  url          = {http://dx.doi.org/10.5281/zenodo.16289}
}

@misc{bergerFILESdlpc28,
  author       = {Matej Kanduc},
  title        = {{{MD} trajectory for DLPC bilayer (Berger, Gromacs 
                   4.5.4), nw=28 w/l}},
  month        = mar,
  year         = 2015,
  doi          = {10.5281/zenodo.16287},
  url          = {http://dx.doi.org/10.5281/zenodo.16287}
}

@misc{salari15,
  author       = {Reza Salari},
  title        = {{PyTopol: A Library For Converting Molecular Topologies}},
  month        = mar,
  year         = 2015,
  doi          = {10.5281/zenodo.16084},
  url          = {http://dx.doi.org/10.5281/zenodo.16084}
}

@article{kulig15,
title = "Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate ",
journal = "Biochim. Biophys. Acta ",
volume = "1848",
number = "2",
pages = "422 - 432",
year = "2015",
note = "",
issn = "0005-2736",
doi = "http://dx.doi.org/10.1016/j.bbamem.2014.10.032",
url = "http://www.sciencedirect.com/science/article/pii/S0005273614003678",
author = "Waldemar Kulig and Piotr Jurkiewicz and Agnieszka Ol{\.z}y{\'n}ska and Joona Tynkkynen and Matti Javanainen and Moutusi Manna and Tomasz R{\'o}g and Martin Hof and Ilpo Vattulainen and Pavel Jungwirth",
}

@misc{GAFFlipidFILESdppc,
  author       = {Ollila Samuli and
                  Retegan, Marius},
  title        = {{{MD} simulation trajectory and related files for 
                   DPPC bilayer (GAFFlipid, Gromacs 4.5)}},
  month        = feb,
  year         = 2015,
  doi          = {10.5281/zenodo.15550},
  url          = {http://dx.doi.org/10.5281/zenodo.15550}
}

@misc{charmmFILESdppc,
  author       = {Ollila Samuli and Miettinen Markus},
  title        = {{{MD} simulation trajectory and related files for DPPC bilayer (CHARMM36, Gromacs 4.5)}},
  month        = feb,
  year         = 2015,
  doi          = {10.5281/zenodo.15549},
  url          = {http://dx.doi.org/10.5281/zenodo.15549}
}

@misc{chiuFILES,
  author       = {Ollila Samuli},
  title        = {{{MD} simulation trajectory and related files for POPC bilayer (Chiu et al. Gromos version, Gromacs 4.5)}},
  month        = feb,
  year         = 2015,
  doi          = {10.5281/zenodo.15548},
  url          = {http://dx.doi.org/10.5281/zenodo.15548}
}

@misc{pogerFILESrf2,
  author       = {Fuchs,  Patrick F.J.},
  title        = {{{MD} simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS53A6\_L, Gromacs 4.0.7, Reaction Field, traj 2)}},
  month        = "jan",
  year         = 2015,
  doi          = {10.5281/zenodo.14591},
  url          = {http://dx.doi.org/10.5281/zenodo.14591}
}

@misc{pogerFILESrf1,
  author       = {Fuchs,  Patrick F.J.},
  title        = {{{MD} simulation trajectory and related files for  DPPC bilayer in full hydration (Poger GROMOS53A6\_L, Gromacs 4.0.7, Reaction Field, traj 1)}},
  month        = jan,
  year         = 2015,
  doi          = {10.5281/zenodo.14592},
  url          = {http://dx.doi.org/10.5281/zenodo.14592}
}

@misc{pogerFILESpme2,
  author       = {Fuchs,  Patrick F.J.},
  title        = {{{MD} simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS53A6\_L, Gromacs 4.0.7, PME, traj 2)}},
  month        = jan,
  year         = 2015,
  doi          = {10.5281/zenodo.14595},
  url          = {http://dx.doi.org/10.5281/zenodo.14595}
}

@misc{pogerFILESpme1,
  author       = {Fuchs,  Patrick F.J.},
  title        = {{{MD} simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS53A6\_L, Gromacs 4.0.7, PME, traj 1)}},
  month        = jan,
  year         = 2015,
  doi          = {10.5281/zenodo.14594},
  url          = {http://dx.doi.org/10.5281/zenodo.14594}
}

@misc{charmm36files50perCHOL,
  author       = {Santuz, Hubert},
  title        = {{{MD} simulation trajectory for POPC/50\% Chol bilayer (CHARMM36, Gromacs 4.5)}},
  month        = jan,
  year         = 2015,
  doi          = {10.5281/zenodo.14068},
  url          = {http://dx.doi.org/10.5281/zenodo.14068}
}

@misc{charmm36files20perCHOL,
  author       = {Santuz, Hubert},
  title        = {{{MD} simulation trajectory for POPC/20\% Chol bilayer (CHARMM36, Gromacs 4.5)}},
  month        = jan,
  year         = 2015,
  doi          = {10.5281/zenodo.14067},
  url          = {http://dx.doi.org/10.5281/zenodo.14067}
}

@misc{charmm36files,
  author       = {Santuz, Hubert},
  title        = {{{MD} simulation trajectory and related files for POPC bilayer (CHARMM36, Gromacs 4.5)}},
  month        = jan,
  year         = 2015,
  doi          = {10.5281/zenodo.14066},
  url          = {http://dx.doi.org/10.5281/zenodo.14066}
}

@misc{charmm36files15wPERl,
      author        = "Ollila O. H. Samuli and Miettinen, Markus",
      title         = "{{MD} simulation trajectory and related files for POPC
                       bilayer in medium low hydration (CHARMM36, Gromacs 4.5)}",
      month         = "Jan",
      year          = "2015",
      doi           = "{10.5281/zenodo.13946}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13946}",
}

@misc{charmm36files7wPERl,
      author        = "Ollila O. H. Samuli and Miettinen, Markus",
      title         = "{{MD} simulation trajectory and related files for POPC bilayer in low hydration  (CHARMM36, Gromacs 4.5)}",
      month         = "Jan",
      year          = "2015",
      doi           = "{10.5281/zenodo.13945}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13945}",
}

@misc{charmm36filesSHORT,
      author        = "Ollila O. H. Samuli and Miettinen, Markus",
      title         = "{{MD} simulation trajectory and related files for POPC bilayer (CHARMM36, Gromacs 4.5)}",
      month         = "Jan",
      year          = "2015",
      doi           = "{10.5281/zenodo.13944}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13944}",
}

@misc{bergerDPPCfiles,
  author       = {M{\"a}{\"a}tt{\"a}, Jukka},
  title        = {DPPC\_Berger},
  month        = jan,
  year         = 2015,
  doi          = {10.5281/zenodo.13934},
  url          = {http://dx.doi.org/10.5281/zenodo.13934}
}

@article {ferrer13,
author = {Salomon-Ferrer, Romelia and Case, David A. and Walker, Ross C.},
title = {An overview of the Amber biomolecular simulation package},
journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
volume = {3},
number = {2},
pages = {198--210},
year = {2013},
}

@Article{silva12,
AUTHOR = {Sousa da Silva, Alan and Vranken, Wim},
TITLE = {ACPYPE - AnteChamber PYthon Parser interfacE},
JOURNAL = {BMC Research Notes},
VOLUME = {5},
YEAR = {2012},
NUMBER = {1},
PAGES = {367},
}

@article{tironi95,
   author = "Tironi, Ilario G. and Sperb, René and Smith, Paul E. and van Gunsteren, Wilfred F.",
   title = "A generalized reaction field method for molecular dynamics simulations",
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   doi = "http://dx.doi.org/10.1063/1.469273" 
}


@article{Plimpton95,
title = "Fast Parallel Algorithms for Short-Range Molecular Dynamics ",
journal = "J. Comput. Phys. ",
volume = "117",
number = "1",
pages = "1 - 19",
year = "1995",
author = "Steve Plimpton"
}

@misc{charmmUAfiles,
      author        = "Alexandru Botan",
      title         = "{DLPC@ 323K, CHARMM36UA force field}",
      month         = "Jan",
      year          = "2015",
      doi           = "{10.5281/zenodo.13821}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13821}",
}

@misc{macrogCHOLfiles,
      author        = "Javanainen, Matti",
      title         = "{POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-%
                       cholesterol. Model by Maciejewski and R{\'o}g}",
      month         = "Jan",
      year          = "2015",
      doi           = "{10.5281/zenodo.13877}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13877}",
}

@misc{gaffDEHYDfiles,
      author        = "O. H. S. Ollila",
      title         = "{{MD} simulation trajectory and related files for POPC bilayer in low hydration (GAFFlipid, Gromacs 4.5)}",
      month         = "Jan",
      year          = "2015",
      doi           = "{10.5281/zenodo.13853}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13853}",
}

@article{jambeck12b,
author = {J{\"a}mbeck, Joakim P. M. and Lyubartsev, Alexander P.},
title = {An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes},
journal = {J. Chem. Theory Comput.},
volume = {8},
number = {8},
pages = {2938-2948},
year = {2012},
}


@misc{bergerDEHYDfiles,
      author        = "O. H. S. Ollila",
      title         = "{{MD} simulation trajectory and related files for POPC bilayer in low hydration (Berger model delivered by Tieleman, Gromacs 4.5)}",
      month         = "Jan",
      year          = "2015",
      doi           = "{10.5281/zenodo.13814}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13814}",
}

@article{Gurtovenko04,
title = "Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study ",
journal = "Biophys. J. ",
volume = "86",
number = "6",
pages = "3461 - 3472",
year = "2004",
author = "Andrey A. Gurtovenko and Michael Patra and Mikko Karttunen and Ilpo Vattulainen"
}

@misc{GAFFlipidFILES,
      author        = "O. H. S. Ollila and Marius Retegan",
      title         = "{{MD} simulation trajectory and related files for POPC bilayer (GAFFlipid, Gromacs 4.5)}",
      month         = "Jan",
      year          = "2015",
      doi           = "{10.5281/zenodo.13791}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13791}",
}

@article{Tieleman99,
title = "An Alamethicin Channel in a Lipid Bilayer: Molecular Dynamics Simulations ",
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volume = "76",
number = "4",
pages = "1757 - 1769",
year = "1999",
author = "D. Peter Tieleman and Herman J.C. Berendsen and Mark S.P. Sansom",
}

@article{Marrink98,
title = "Adhesion Forces of Lipids in a Phospholipid Membrane Studied by Molecular Dynamics Simulations ",
journal = "Biophys. J. ",
volume = "74",
number = "2",
pages = "931 - 943",
year = "1998",
author = "Siewert-Jan Marrink and Oliver Berger and Peter Tieleman and Fritz J{\"a}hnig"
}

@misc{fuchs14, 
title={Poger lipids with Reaction Field using different GROMACS versions}, 
url={http://www.dsimb.inserm.fr/~fuchs/project_Samuli/Poger_DPPC/tests_gmx_versions/Comments_area_different_gmx_versions.pdf}, 
DOI={}, 
author={Patrick Fuchs}, 
year={2014}} 

@misc{pogerFILES, 
title={Temporary location for simulations files with Poger et al. model.}, 
url={http://www.dsimb.inserm.fr/~fuchs/project_Samuli/Poger_DPPC/}, 
DOI={}, 
author={Patrick Fuchs}, 
year={2014}} 

@misc{macrogdehydFILES,
      author        = "Javanainen, Matti",
      title         = "{POPC @ 310K, varying water-to-lipid ratio. Model by
                       Maciejewski and R{\'o}g}",
      month         = "Dec",
      year          = "2014",
      doi           = "{10.5281/zenodo.13498}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13498}",
}

@misc{macrogFILES,
      author        = "Javanainen, Matti",
      title         = "{POPC @ 310K, model by Maciejewski and R{\'o}g}",
      month         = "Dec",
      year          = "2014",
      doi           = "{10.5281/zenodo.13497}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13497}",
}

@misc{ulmschneiderFILES,
      author        = "Javanainen, Matti",
      title         = "{POPC @ 310K, Model by Ulmschneider and Ulmschneider}",
      month         = "Dec",
      year          = "2014",
      doi           = "{10.5281/zenodo.13392}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13392}",
}

@misc{kukolFILES,
      author        = "Javanainen, Matti",
      title         = "{POPC @ 298K, Model by Kukol}",
      month         = "Dec",
      year          = "2014",
      doi           = "{10.5281/zenodo.13393}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13393}",
}

@misc{bergerFILESpopc,
      journal       = {Zenodo},  
      author        = {O. H. S. Ollila and Tiago Ferreira and Daniel Topgaard},
      title         = "{MD simulation trajectory and related files for POPC bilayer (Berger model delivered by Tieleman, Gromacs 4.5)}",
      month         = Dec,
      year          = 2014,
      doi           = {10.5281/zenodo.13279},
      url           = {http://dx.doi.org/10.5281/zenodo.13279},
archivePrefix = "arXiv",
}

@misc{ollila13,
   author = {O. H. Samuli Ollila},
    title = {Response of the hydrophilic part of lipid membranes to changing conditions - a critical comparison of simulations to experiments},
  journal = {ArXiv e-prints},
archivePrefix = "arXiv",
   eprint = {1309.2131v1},
 primaryClass = "physics.bio-ph",
 keywords = {Physics - Biological Physics, Condensed Matter - Soft Condensed Matter, Quantitative Biology - Biomolecules},
     year = 2013,
    month = sep,
   url = {http://arxiv.org/abs/1309.2131v1},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{gowers09,
author = {Timothy Gowers and Michael Nielsen},
title = {Massively collaborative mathematics},
journal = {Nature},
volume = {461},
number = {},
pages = {879-881},
year = {2009},
}

@article{akutsu81b,
author = {Akutsu, Hideo},
title = {Direct determination by Raman scattering of the conformation of the choline group in phospholipid bilayers},
journal = {Biochemistry},
volume = {20},
number = {26},
pages = {7359-7366},
year = {1981},
}

@article {essex94,
	author = {Essex, Jonathan W. and Hann, Michael M. and Richards, W. Graham},
	title = {Molecular Dynamics Simulation of a Hydrated Phospholipid Bilayer},
	volume = {344},
	number = {1309},
	pages = {239--260},
	year = {1994},
	journal = {Philos. T. Roy. Soc. B}
}

@misc{dmpcFILES,
author = "Markus S. Miettinen",
title = "{Molecular dynamics simulation trajectory of a fully hydrated DMPC lipid bilayer}",
year = "2013",
month = "10",
url = "http://dx.doi.org/10.6084/m9.figshare.829642"
}

@article{miettinen09,
author = {Miettinen, Markus S. and Gurtovenko, Andrey A. and Vattulainen, Ilpo and Karttunen, Mikko},
title = {Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions},
journal = {J. Phys. Chem. B},
volume = {113},
number = {27},
pages = {9226-9234},
year = {2009},
}

@article{Kulig14b,
title = "Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate ",
journal = "Biochim. Biophys. Acta ",
volume = "1848",
number = "2",
pages = "422 - 432",
year = "2015",
author = "Waldemar Kulig and Piotr Jurkiewicz and Agnieszka Olżyńska and Joona Tynkkynen and Matti Javanainen and Moutusi Manna and Tomasz R{\'o}g and Martin Hof and Ilpo Vattulainen and Pavel Jungwirth",
}


@article{Hauser81b,
title = "Preferred conformation and molecular packing of phosphatidylethanolamine and phosphatidylcholine ",
journal = "Biochim. Biophys. Acta ",
volume = "650",
number = "1",
pages = "21 - 51",
year = "1981",
author = "H. Hauser and I. Pascher and R.H. Pearson and S. Sundell"
}

@misc{slipidsFILESpopc,
  author       = {Javanainen, Matti},
  title        = {POPC @ 310K, Slipids force field.},
  month        = jan,
  year         = 2015,
  doi          = {10.5281/zenodo.13887},
  url          = {http://dx.doi.org/10.5281/zenodo.13887}
}

@misc{slipidsFILES,
      author        = "M{\"a}{\"a}tt{\"a}, Jukka",
      title         = "{DPPC\_Slipids}",
      month         = "Dec",
      year          = "2014",
      doi           = "{10.5281/zenodo.13287}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13287}",
}

@misc{bergerFILESpopc60chol,
      author        = "O. H. S. Ollila and Tiago Ferreira and Daniel Topgaard",
      title         = "{MD simulation trajectory and related files for POPC/cholesterol (60 mol\%) bilayer (Berger model delivered by Tieleman, modified H{\"o}ltje, Gromacs 4.5)}",
      month         = "Dec",
      year          = "2014",
      doi           = "{10.5281/zenodo.13286}",
      url           = "{http://dx.doi.org/10.5281/zenodo.13286}",
}

@misc{bergerFILESpopc50chol,
      author        = "O. H. S. Ollila and Tiago Ferreira and Daniel Topgaard",
      title         = "{MD simulation trajectory and related files for POPC/cholesterol (50 mol\%) bilayer (Berger model delivered by Tieleman, modified H{\"o}ltje, Gromacs 4.5)}",
      month         = "Dec",
      year          = "2014",
      doi           = "{10.5281/zenodo.13285}",
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}

@misc{bergerFILESpopc34chol,
      author        = "O. H. S. Ollila and Tiago Ferreira and Daniel Topgaard",
      title         = "{MD simulation trajectory and related files for POPC/cholesterol (34 mol\%) bilayer (Berger model delivered by Tieleman, modified H{\"o}ltje, Gromacs 4.5)}",
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@misc{bergerFILESpopc15chol,
      author        = "O. H. S. Ollila and Tiago Ferreira and Daniel Topgaard",
      title         = "{MD simulation trajectory and related files for POPC/cholesterol (15 mol\%) bilayer (Berger model delivered by Tieleman, modified H{\"o}ltje, Gromacs 4.5)}",
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@misc{bergerFILESpopc7chol,
      author        = "O. H. S. Ollila and Tiago Ferreira and Daniel Topgaard",
      title         = "{MD simulation trajectory and related files for POPC/cholesterol (7 mol\%) bilayer (Berger model delivered by Tieleman, modified H{\"o}ltje, Gromacs 4.5)}",
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@misc{tjornhammarfiles, 
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@misc{lipid14files, 
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%title={Dynamical Aspects of Polyunsaturated Lipid Bilayers},
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author={},
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@misc{HGmodelFILES,
author={},
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@misc{abbreviations,
author={},
title={},
howpublished={},
month={},
year={},
note={HDL High Density Lipoprotein; LDL Low Density Lipoprotein; LCAT Lecithin-Cholesterol AcylTransferase; CETP Cholesteryl Ester Transfer Protein; POPC Palmitoyl-Oleoyl PhosphatidylCholine; DLPC Di-Linoleoyl PhosphatidylCholine; CHES Cholesteryl Oleate; TRIOL Trioleate; CHOL Unesterified Cholesterol; LysoPC LysoPhosphatidylcholine},
key={},
url={},
abstract={},
}

@misc{abbreviationsNEW,
note={Abbreviations used in this article are as follows:
LCAT (lecithin-cholesterol acyltransferase), 
CETP (cholesteryl ester transfer protein), 
HDL (high density lipoprotein), 
LDL (low density lipoprotein), 
CHOL ((unesterified) cholesterol), 
CHES (cholesteryl ester), 
PC (phosphatidylcholine), 
POPC (palmitoyloleoyl-PC), 
DLPC (dilinoleoyl-PC), 
Lyso-PC (lyso-PC), 
TG (triglyceride)},
}

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  journal	= {Annu Rev Biophys Biomol Struct.},
  year	= 2006,
  volume	= 35,
  pages	= {177-198},
}

@Article{Cur07,
  author	= {J. Curdova and P. Capkova and J. Plasek and 
                   J. Repakova and I. Vattulainen}, 
  title	= {Free Pyrene Probes in Gel and Fluid Membranes: Perspective 
           Through Atomistic Simulations},
  journal	= {J. Phys. Chem. B},
  year	= 2007,
  volume	= 111,
  pages	= {3640},
}

@article{patra07,
AUTHOR={M. Patra and M. Hyvonen and E. Falck and M. Sabouri-Ghomi and 
        I. Vattulainen and M. Karttunen},
TITLE={Long-range interactions and parallel scalability in molecular 
       simulations},
JOURNAL={Comput. Phys. Commun.},
YEAR={2007},
volume={176},
pages={14-22}
}


@article{Musgaard10,
title = "Modeling the Membrane Role in Ca2+-ATPase Catalytic Cycle",
journal = "Biophys. J.",
volume = "98",
number = "",
pages = "487a - 487a",
year = "2010",
note = "",
issn = "0006-3495",
doi = "DOI: 10.1016/j.bpj.2009.12.2652",
url = "http://www.sciencedirect.com/science/article/B94RW-4Y7W930-366/2/0dedb4149ee14b2a239532b418ee4258",
author = "Maria Musgaard and Jesper V. Møller and Poul Nissen and Lea Thøgersen and Birgit Schiøtt"
}









@InProceedings{   Vattulainen-diffusion04, 
  author        = {I. Vattulainen and O. G. Mouritsen},
  title         = {Diffusion in Membranes},
  booktitle     = {Diffusion in Condensed Matter: Methods, Materials, Models},
  pages         = {},
  year          = 2004,
  editor        = {P. Heitjans and J. Karger},
  volume        = 2,
  publisher     = {Springer-Verlag},
  address       = {Berlin}
}


@Article{joung2008determination,
  title={Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations},
  author={Joung, In Suk and Cheatham III, Thomas E},
  journal={The journal of physical chemistry B},
  volume={112},
  number={30},
  pages={9020--9041},
  year={2008},
  publisher={ACS Publications}
}


@article{LipidFingerprints2018,
author = {Corradi, Valentina and Mendez-Villuendas, Eduardo and Ingólfsson, Helgi I. and Gu, Ruo-Xu and Siuda, Iwona and Melo, Manuel N. and Moussatova, Anastassiia and DeGagné, Lucien J. and Sejdiu, Besian I. and Singh, Gurpreet and Wassenaar, Tsjerk A. and Delgado Magnero, Karelia and Marrink, Siewert J. and Tieleman, D. Peter},
title = {Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins},
journal = {ACS Central Science},
volume = {4},
number = {6},
pages = {709-717},
year = {2018},
doi = {10.1021/acscentsci.8b00143},
    note ={PMID: 29974066},

URL = { 
        https://doi.org/10.1021/acscentsci.8b00143
    
},
eprint = { 
        https://doi.org/10.1021/acscentsci.8b00143
    
}

}

%---EOF


%---2---Book
%
%\cites{author1}{author2}{year}
%\cite{author1:author2:year}
@book{author1:author2:year,
AUTHOR={author1 and author2},
EDITOR={},
TITLE={},
PUBLISHER={},
YEAR={},
volume={},
number={}, 
series={},
address={},
edition={},
month={},
note={},
key={},
url={},
abstract={},
}

%---3---Booklet
%
%\cites{title}{year}
%\cite{title:year}
@booklet{title:year,
TITLE={},
author={},
howpublished={},
address={},
month={},
year={},
note={},
key={},
url={},
abstract={},
}

%---4---Conference
%
%-(same as Inproceeding)
%

%---5---Inbook
%
%\cites{author}{year}
%\cite{author}{year}
@inbook{author:year,
AUTHOR={},
EDITOR={},
TITLE={},
CHAPTER={},
PAGES={},
PUBLISHER={},
YEAR={},
volume={},
number={}, 
series={},
type={},
address={},
edition={},
month={},
note={},
key={},
url={},
abstract={},
}

%---6---Incollection
%
%
%\cites{author1}{author2}{year}
%\cite{author1:author2:year}
@incollection{author1:author2:year,
AUTHOR={},
TITLE={},
BOOKTITLE={},
PUBLISHER={},
YEAR={},
editor={},
volume={},
number={}, 
series={},
type={},
chapter={},
pages={},
address={},
edition={},
month={},
note={},
key={},
url={},
abstract={},
}

%---7---Inproccedings
%
%\cites{author1}{author2}{year}
%\cite{author1:author2:year}
@inproceedings{author1:author2:year,
AUTHOR={},
TITLE={},
BOOKTITLE={},
YEAR={},
editor={},
volume={},
number={}, 
series={},
pages={},
address={},
month={},
organization={},
publisher={},
note={},
key={},
url={},
abstract={},
}

%---8---Manual
%
%cite{title}
@manual{,
TITLE={},
author={},
address={},
edition={},
month={},
year={},
note={},
key={},
url={},
abstract={},
}

%---9---Master's-Thesis
%
%\cites{author}{2000},
%\cite{author:year,
@mastersthesis{author:year,
AUTHOR={},
TITLE={},
SCHOOL={},
YEAR={},
type={},
address={},
month={},
note={},
key={},
url={},
abstract={},
}

%---10---Misc
%
%\cite{author:year}
@misc{author:year,
author={author},
title={},
howpublished={},
month={},
year={},
note={},
key={},
url={},
abstract={},
}

%---11---PhD-Thesis
%
%\cites{author}{2000},
%\cite{author:year,
@phdthesis{author:year,
AUTHOR={},
TITLE={},
SCHOOL={},
YEAR={},
type={},
address={},
month={},
note={},
key={},
url={},
abstract={},
}

%---12--Proceeding
%
%\cites{Title}{year}
%\cite{Title:year}
@proceedings{Title:year,
TITLE={Title},
YEAR={},
editor={},
volume={},
number={},
series={},
address={},
month={},
organization={},
publisher={},
note={},
key={},
url={},
abstract={},
}

%---13---Techreport
%
%\cites{author:year}
%\cite{author:year}
@techreport{author:year,
AUTHOR={},
TITLE={},
INSTITUTION={},
YEAR={},
type={},
number={},
address={},
month={},
note={},
key={},
url={},
abstract={},
}

%---14---Unpublished
%
%\cites{author}{year}
%\cite{author:year}
@unpublished{author:year,
AUTHOR={},
TITLE={},
NOTE={},
month={},
year={},
key={},
url={},
abstract={},
}

%---15---Standard
%
%\cited{name}{no}{year}
%\cite{name:no:year}
@standard{name:no:year,
TITLE={name},
ORGANIZATION={},
VOLUME={},
NUMBER={no},
YEAR={year},
editor={},
series={},
pages={},
address={},
month={},
note={},
key={},
url={},
abstract={},
}
@article{author1:year,
AUTHOR={author1 and author2 and author3},
TITLE={},
JOURNAL={},
YEAR={},
volume={},
number={},
pages={},
month={},
note={},
key={},
url={},
abstract={},
}
%---EOF