references.bib

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title = {The ugly, bad, and good stories of large-scale biomolecular simulations},
journal = {Current Opinion in Structural Biology},
volume = {73},
pages = {102338},
year = {2022},
author = {Chitrak Gupta and Daipayan Sarkar and D. Peter Tieleman and Abhishek Singharoy},
}

@article{seelig87,
author = {Seelig, Joachim and MacDonald, Peter M. and Scherer, Peter G.},
title = {Phospholipid head groups as sensors of electric charge in membranes},
journal = {Biochemistry},
volume = {26},
number = {24},
pages = {7535-7541},
year = {1987},
}

@article{piggot12,
author = {Piggot, Thomas J. and Pi{\~n}eiro, {\'A}ngel and Khalid, Syma},
title = {Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study},
journal = {J. Chem. Theory Comput.},
volume = {8},
number = {11},
pages = {4593-4609},
year = {2012},
}

@article{kukol09,
author = {Kukol, Andreas},
title = {Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins},
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volume = {5},
number = {3},
pages = {615-626},
year = {2009},
}

@article{Chandrasekhar03,
year={2003},
issn={0175-7571},
journal={Eur. Biophys. J.},
volume={32},
issue={1},
title={A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field},
author={Chandrasekhar, Indira and Kastenholz, Mika and Lins, RobertoD. and Oostenbrink, Chris and Schuler, LukasD. and Tieleman, D.Peter and Gunsteren, WilfredF.},
pages={67-77},
language={English}
}


@article{roos19,
author = {Roos, Katarina and Wu, Chuanjie and Damm, Wolfgang and Reboul, Mark and Stevenson, James M. and Lu, Chao and Dahlgren, Markus K. and Mondal, Sayan and Chen, Wei and Wang, Lingle and Abel, Robert and Friesner, Richard A. and Harder, Edward D.},
title = {OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules},
journal = {Journal of Chemical Theory and Computation},
volume = {15},
number = {3},
pages = {1863-1874},
year = {2019},
}

@article{Salsbury22,
author = {Salsbury, Alexa M. and Michel, Haley M. and Lemkul, Justin A.},
title = {Ion-Dependent Conformational Plasticity of Telomeric G-Hairpins and G-Quadruplexes},
journal = {ACS Omega},
volume = {7},
number = {27},
pages = {23368-23379},
year = {2022},
doi = {10.1021/acsomega.2c01600},

URL = { 
    
        https://doi.org/10.1021/acsomega.2c01600
    
    

},
eprint = { 
    
        https://doi.org/10.1021/acsomega.2c01600
    
    

}

}

@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 = {The Journal of Chemical Physics},
    volume = {153},
    number = {5},
    pages = {050901},
    year = {2020},
    month = {08},
}

@article{nencini22,
author = {Nencini, Ricky and Ollila, O. H. Samuli},
title = {Charged Small Molecule Binding to Membranes in MD Simulations Evaluated against NMR Experiments},
journal = {The Journal of Physical Chemistry B},
volume = {126},
number = {36},
pages = {6955-6963},
year = {2022},
}

@article{ferreira15,
   author = "Ferreira, Tiago Mendes and Ollila, O. H. Samuli and Pigliapochi, Roberta and Dabkowska, Aleksandra P. and Topgaard, Daniel",
   title = "Model-free estimation of the effective correlation time for {C}-{H} bond reorientation in amphiphilic bilayers: $^1${H}-$^{13}${C} solid-state {NMR} and {MD} simulations",
   journal = "J. Chem. Phys.",
   year = "2015",
   volume = "142",
   pages = "044905",
}


@article{ollila07,
AUTHOR={S. Ollila and M. T. Hyv{\"o}nen and  I. Vattulainen},
TITLE={Polyunsaturation in Lipid Membranes: Dynamic Properties and Lateral Pressure Profiles},
JOURNAL={J. Phys. Chem. B},
YEAR={2007},
volume={111},
pages={3139-3150},
month={},
note={},
key={},
url={},
abstract={},
}


@article{ollila16,
title = "Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments ",
journal = "Biochim. Biophys. Acta",
volume = "1858",
number = "10",
pages = "2512 - 2528",
year = "2016",
author = "O.H. Samuli Ollila and Georg Pabst",
}

@article{bacle21,
author = {Bacle, Amélie and Buslaev, Pavel and Garcia-Fandino, Rebeca and Favela-Rosales, Fernando and Mendes Ferreira, Tiago and Fuchs, Patrick F. J. and Gushchin, Ivan and Javanainen, Matti and Kiirikki, Anne M. and Madsen, Jesper J. and Melcr, Josef and Milán Rodríguez, Paula and Miettinen, Markus S. and Ollila, O. H. Samuli and Papadopoulos, Chris G. and Peón, Antonio and Piggot, Thomas J. and Piñeiro, Ángel and Virtanen, Salla I.},
title = {Inverse Conformational Selection in Lipid–Protein Binding},
journal = {Journal of the American Chemical Society},
volume = {143},
number = {34},
pages = {13701-13709},
year = {2021},
}

@article{NMRlipidsIII,
author = {Javanainen, Matti and Heftberger, Peter and Madsen, Jesper J. and Miettinen, Markus S. and Pabst, Georg and Ollila, O. H. Samuli},
title = {Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions},
journal = {Journal of Chemical Theory and Computation},
volume = {19},
number = {18},
pages = {6342-6352},
year = {2023},
}

@Article{ferreira13,
author ="Ferreira, Tiago Mendes and Coreta-Gomes, Filipe and Ollila, O. H. Samuli and Moreno, Maria Joao and Vaz, Winchil L. C. and Topgaard, Daniel",
title  ="Cholesterol and {POPC} segmental order parameters in lipid membranes: solid state $^1${H}-$^{13}${C} {NMR} and {MD} simulation studies",
journal  ="Phys. Chem. Chem. Phys.",
year  ="2013",
volume  ="15",
issue  ="6",
pages  ="1976-1989"
}

@article{kucerka2015,
author = {Kučerka, Norbert and van Oosten, Brad and Pan, Jianjun and Heberle, Frederick A. and Harroun, Thad A. and Katsaras, John},
title = {Molecular Structures of Fluid Phosphatidylethanolamine Bilayers Obtained from Simulation-to-Experiment Comparisons and Experimental Scattering Density Profiles},
journal = {The Journal of Physical Chemistry B},
volume = {119},
number = {5},
pages = {1947-1956},
year = {2015},
}


@article{Melcr:2018a,
	Author = {Melcr, Josef and Martinez-Seara, Hector and Nencini, Ricky and Kolafa, Ji{\v r}{\'\i} and Jungwirth, Pavel and Ollila, O. H. Samuli},
	Journal = {J. Phys. Chem. B},
	Pages = {4546--4557},
	Title = {Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization},
	Volume = {122},
	Year = {2018}
}
@article{lucas2012charge,
  title={Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems},
  author={Lucas, Timothy R and Bauer, Brad A and Patel, Sandeep},
  journal={Biochimica et Biophysica Acta (BBA)-Biomembranes},
  volume={1818},
  number={2},
  pages={318--329},
  year={2012},
  publisher={Elsevier}
}
@article{li2017drude,
  title={Drude polarizable force field for molecular dynamics simulations of saturated and unsaturated zwitterionic lipids},
  author={Li, Hui and Chowdhary, Janamejaya and Huang, Lei and He, Xibing and MacKerell Jr, Alexander D and Roux, Beno{\^\i}t},
  journal={Journal of chemical theory and computation},
  volume={13},
  number={9},
  pages={4535--4552},
  year={2017},
  publisher={ACS Publications}
}

@article{Li23chol,
author = {Yan Li and Ye Liu and Boya Yang and Guohui Li and Huiying Chu},
title = {Polarizable atomic multipole-based force field for cholesterol},
journal = {Journal of Biomolecular Structure and Dynamics},
volume = {0},
number = {0},
pages = {1-11},
year  = {2023},
publisher = {Taylor & Francis},
doi = {10.1080/07391102.2023.2245045},
  

URL = { 
    
        https://doi.org/10.1080/07391102.2023.2245045
    
    

},
eprint = { 
    
        https://doi.org/10.1080/07391102.2023.2245045
    
    

}

}
@article{klauda2010update,
  title={Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types},
  author={Klauda, Jeffery B and Venable, Richard M and Freites, J Alfredo and O’Connor, Joseph W and Tobias, Douglas J and Mondragon-Ramirez, Carlos and Vorobyov, Igor and MacKerell Jr, Alexander D and Pastor, Richard W},
  journal={The journal of physical chemistry B},
  volume={114},
  number={23},
  pages={7830--7843},
  year={2010},
  publisher={ACS Publications}
}



@article{seelig1974dynamic,
  title={Dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance},
  author={Seelig, Anna and Seelig, Joachim},
  journal={Biochemistry},
  volume={13},
  number={23},
  pages={4839--4845},
  year={1974},
  publisher={ACS Publications}
}
@article{seelig1975bilayers,
  title={Bilayers of dipalmitoyl-3-sn-phosphatidylcholine: Conformational differences between the fatty acyl chains},
  author={Seelig, Anna and Seelig, Joachim},
  journal={Biochimica et Biophysica Acta (BBA)-Biomembranes},
  volume={406},
  number={1},
  pages={1--5},
  year={1975},
  publisher={Elsevier}
}
@article{gally1975conformation,
  title={Conformation and motion of the choline head group in bilayers of dipalmitoyl-3-sn-phosphatidylcholine},
  author={Gally, Hans U and Niederberger, Werner and Seelig, Joachim},
  journal={Biochemistry},
  volume={14},
  number={16},
  pages={3647--3652},
  year={1975},
  publisher={ACS Publications}
}
@article{gally1981structure,
  title={Structure of Escherichia coli membranes. Glycerol auxotrophs as a tool for the analysis of the phospholipid head-group region by deuterium magnetic resonance},
  author={Gally, Hans Ulrich and Pluschke, Gerd and Overath, Peter and Seelig, Joachim},
  journal={Biochemistry},
  volume={20},
  number={7},
  pages={1826--1831},
  year={1981},
  publisher={ACS Publications}
}

@article{roux2011ion,
  title={Ion selectivity in channels and transporters},
  author={Roux, Beno{\^\i}t and Bern{\`e}che, Simon and Egwolf, Bernhard and Lev, Bogdan and Noskov, Sergei Y and Rowley, Christopher N and Yu, Haibo},
  journal={Journal of general physiology},
  volume={137},
  number={5},
  pages={415--426},
  year={2011},
  publisher={The Rockefeller University Press}
}


@article{strenk1985model,
  title={A model of orientational ordering in phosphatidylcholine bilayers based on conformational analysis of the glycerol backbone region},
  author={Strenk, LM and Westerman, PW and Doane, JW},
  journal={Biophysical journal},
  volume={48},
  number={5},
  pages={765--773},
  year={1985},
  publisher={Elsevier}
}
@article{seelig1978molecular,
  title={Molecular order in cis and trans unsaturated phospholipid bilayers},
  author={Seelig, Joachim and Waespe-Sarcevic, Nada},
  journal={Biochemistry},
  volume={17},
  number={16},
  pages={3310--3315},
  year={1978},
  publisher={ACS Publications}
}
@article{shi2011hydration,
author = {Shi, Yue and Wu, Chuanjie and Ponder, Jay W. and Ren, Pengyu},
title = {Multipole electrostatics in hydration free energy calculations},
journal = {Journal of Computational Chemistry},
volume = {32},
number = {5},
pages = {967-977},
keywords = {hydration free energy, polarizable force field, multipole eletrostatics},
doi = {https://doi.org/10.1002/jcc.21681},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21681},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.21681},
abstract = {Abstract Hydration free energy (HFE) is generally used for evaluating molecular solubility, which is an important property for pharmaceutical and chemical engineering processes. Accurately predicting HFE is also recognized as one fundamental capability of molecular mechanics force field. Here, we present a systematic investigation on HFE calculations with AMOEBA polarizable force field at various parameterization and simulation conditions. The HFEs of seven small organic molecules have been obtained alchemically using the Bennett Acceptance Ratio method. We have compared two approaches to derive the atomic multipoles from quantum mechanical calculations: one directly from the new distributed multipole analysis and the other involving fitting to the electrostatic potential around the molecules. Wave functions solved at the MP2 level with four basis sets (6-311G*, 6-311++G(2d,2p), cc-pVTZ, and aug-cc-pVTZ) are used to derive the atomic multipoles. HFEs from all four basis sets show a reasonable agreement with experimental data (root mean square error 0.63 kcal/mol for aug-cc-pVTZ). We conclude that aug-cc-pVTZ gives the best performance when used with AMOEBA, and 6-311++G(2d,2p) is comparable but more efficient for larger systems. The results suggest that the inclusion of diffuse basis functions is important for capturing intermolecular interactions. The effect of long-range correction to van der Waals interaction on the hydration free energies is about 0.1 kcal/mol when the cutoff is 12Å, and increases linearly with the number of atoms in the solute/ligand. In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed-charge water in the HFE calculation. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011},
year = {2011}
}


@article{shi2013proteinamoeba,
author = {Shi, Yue and Xia, Zhen and Zhang, Jiajing and Best, Robert and Wu, Chuanjie and Ponder, Jay W. and Ren, Pengyu},
title = {Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {9},
pages = {4046-4063},
year = {2013},
doi = {10.1021/ct4003702},
   

URL = { 
        https://doi.org/10.1021/ct4003702
    
},
eprint = { 
        https://doi.org/10.1021/ct4003702
    
}

}



@article{sun2017,
author = {Sun, Rui-Ning and Gong, Haipeng},
title = {Simulating the Activation of Voltage Sensing Domain for a Voltage-Gated Sodium Channel Using Polarizable Force Field},
journal = {The Journal of Physical Chemistry Letters},
volume = {8},
number = {5},
pages = {901-908},
year = {2017},
doi = {10.1021/acs.jpclett.7b00023},
  


URL = { 
        https://doi.org/10.1021/acs.jpclett.7b00023},
eprint = { 
        https://doi.org/10.1021/acs.jpclett.7b00023
    
}

}


@article{douliez1995restatement,
  title={Restatement of order parameters in biomembranes: calculation of CC bond order parameters from CD quadrupolar splittings},
  author={Douliez, Jean-Paul and Leonard, Alain and Dufourc, Erick J},
  journal={Biophysical journal},
  volume={68},
  number={5},
  pages={1727--1739},
  year={1995},
  publisher={Elsevier}
}
@article{shaikh2002monounsaturated,
  title={Monounsaturated PE does not phase-separate from the lipid raft molecules sphingomyelin and cholesterol: role for polyunsaturation?},
  author={Shaikh, Saame Raza and Brzustowicz, Michael R and Gustafson, Noah and Stillwell, William and Wassall, Stephen R},
  journal={Biochemistry},
  volume={41},
  number={34},
  pages={10593--10602},
  year={2002},
  publisher={ACS Publications}
}
@article{perly1985acyl,
  title={Acyl chain dynamics of phosphatidylethanolamines containing oleic acid and dihydrosterculic acid: deuteron NMR relaxation studies},
  author={Perly, Bruno and Smith, Ian CP and Jarrell, Harold C},
  journal={Biochemistry},
  volume={24},
  number={17},
  pages={4659--4665},
  year={1985},
  publisher={ACS Publications}
}
@article{chu2018polarizable,
  title={Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids},
  author={Chu, Huiying and Peng, Xiangda and Li, Yan and Zhang, Yuebin and Min, Hanyi and Li, Guohui},
  journal={Molecular Physics},
  volume={116},
  number={7-8},
  pages={1037--1050},
  year={2018},
  publisher={Taylor \& Francis}
}
@article{chu2018anionicpolarizable,
  title={A polarizable atomic multipole-based force field for molecular dynamics simulations of anionic lipids},
  author={Chu, Huiying and Peng, Xiangda and Li, Yan and Zhang, Yuebin and Li, Guohui},
  journal={Molecules},
  volume={23},
  number={1},
  pages={77},
  year={2018},
  publisher={Multidisciplinary Digital Publishing Institute}
}
@article{davis2009molecular,
  title={Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models},
  author={Davis, Joseph E and Rahaman, Obaidur and Patel, Sandeep},
  journal={Biophysical journal},
  volume={96},
  number={2},
  pages={385--402},
  year={2009},
  publisher={Elsevier}
}
@article{klauda2005ab,
  title={An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer},
  author={Klauda, Jeffery B and Brooks, Bernard R and MacKerell, Alexander D and Venable, Richard M and Pastor, Richard W},
  journal={The journal of physical chemistry B},
  volume={109},
  number={11},
  pages={5300--5311},
  year={2005},
  publisher={ACS Publications}
}
@article{davis2009charge,
  title={Charge equilibration force fields for lipid environments: applications to fully hydrated DPPC bilayers and DMPC-embedded gramicidin A},
  author={Davis, Joseph E and Patel, Sandeep},
  journal={The Journal of Physical Chemistry B},
  volume={113},
  number={27},
  pages={9183--9196},
  year={2009},
  publisher={ACS Publications}
}
@article{melcr2019improved,
	title={Improved Cation Binding to Lipid Bilayers with Negatively Charged POPS by Effective Inclusion of Electronic Polarization},
	author={Melcr, Josef and Ferreira, Tiago M and Jungwirth, Pavel and Ollila, OH Samuli},
	journal={Journal of chemical theory and computation},
	year={2019},
	publisher={ACS Publications}
}

@article{Botan2015,
author = {Botan, Alexandru and Favela-Rosales, Fernando and Fuchs, Patrick F. J. and Javanainen, Matti and Kanduč, Matej and Kulig, Waldemar and Lamberg, Antti and Loison, Claire and Lyubartsev, Alexander and Miettinen, Markus S. and Monticelli, Luca and Määttä, Jukka and Ollila, O. H. Samuli and Retegan, Marius and Róg, Tomasz and Santuz, Hubert and Tynkkynen, Joona},
title = {Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions},
journal = {The Journal of Physical Chemistry B},
volume = {119},
number = {49},
pages = {15075-15088},
year = {2015},
doi = {10.1021/acs.jpcb.5b04878},


URL = { 
        https://doi.org/10.1021/acs.jpcb.5b04878
    
},
eprint = { 
        https://doi.org/10.1021/acs.jpcb.5b04878
    
}

}

@Inbook{Antila2013,
author="Antila, Hanne S.
and Salonen, Emppu",
editor="Monticelli, Luca
and Salonen, Emppu",
title="Polarizable Force Fields",
bookTitle="Biomolecular Simulations: Methods and Protocols",
year="2013",
publisher="Humana Press",
address="Totowa, NJ",
pages="215--241",
abstract="This chapter provides an overview of the most common methods for including an explicit description of electronic polarization in molecular mechanics force fields: the induced point dipole, shell, and fluctuating charge models. The importance of including polarization effects in biomolecular simulations is discussed, and some of the most important achievements in the development of polarizable biomolecular force fields to date are highlighted.",
isbn="978-1-62703-017-5",
doi="10.1007/978-1-62703-017-5_9",
url="https://doi.org/10.1007/978-1-62703-017-5_9"
}

@article{Antila2019,
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 = {The Journal of Physical Chemistry B},
volume = {123},
number = {43},
pages = {9066-9079},
year = {2019},
doi = {10.1021/acs.jpcb.9b06091},
    

URL = { 
        https://doi.org/10.1021/acs.jpcb.9b06091
    
},
eprint = { 
        https://doi.org/10.1021/acs.jpcb.9b06091
    
}

}

@article{Antila2021,
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 = {Journal of Chemical Information and Modeling},
volume = {61},
number = {2},
pages = {938-949},
year = {2021},
doi = {10.1021/acs.jcim.0c01299},
   

URL = { 
        https://doi.org/10.1021/acs.jcim.0c01299
    
},
eprint = { 
        https://doi.org/10.1021/acs.jcim.0c01299
    
}

}
@article{Antila2022,
author = {Antila, Hanne S. and Kav, Batuhan and Miettinen, Markus S. and Martinez-Seara, Hector and Jungwirth, Pavel and Ollila, O. H. Samuli},
title = {Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks},
journal = {The Journal of Physical Chemistry B},
volume = {126},
number = {23},
pages = {4169-4183},
year = {2022},
doi = {10.1021/acs.jpcb.2c01954},

URL = { 
        https://doi.org/10.1021/acs.jpcb.2c01954
    
},
eprint = { 
        https://doi.org/10.1021/acs.jpcb.2c01954
    
}

}

@article{Antila2022rot,
title = {Rotational decoupling between the hydrophilic and hydrophobic regions in lipid membranes},
journal = {Biophysical Journal},
volume = {121},
number = {1},
pages = {68-78},
year = {2022},
issn = {0006-3495},
doi = {https://doi.org/10.1016/j.bpj.2021.12.003},
url = {https://www.sciencedirect.com/science/article/pii/S0006349521038947},
author = {Hanne S. Antila and Anika Wurl and O.H. Samuli Ollila and Markus S. Miettinen and Tiago M. Ferreira},
abstract = {Cells use homeostatic mechanisms to ensure an optimal composition of distinct types of lipids in cellular membranes. The hydrophilic region of biological lipid membranes is mainly composed of several types of phospholipid headgroups that interact with incoming molecules, nanoparticles, and viruses, whereas the hydrophobic region consists of a distribution of acyl chains and sterols affecting membrane fluidity/rigidity related properties and forming an environment for membrane-bound molecules such as transmembrane proteins. A fundamental open question is to what extent the motions of these regions are coupled and, consequently, how strongly the interactions of phospholipid headgroups with other molecules depend on the properties and composition of the membrane hydrophobic core. We combine advanced solid-state nuclear magnetic resonance spectroscopy with high-fidelity molecular dynamics simulations to demonstrate how the rotational dynamics of choline headgroups remain nearly unchanged (slightly faster) with incorporation of cholesterol into a phospholipid membrane, contrasting the well-known extreme slowdown of the other phospholipid segments. Notably, our results suggest a new paradigm in which phospholipid dipole headgroups interact as quasi-freely rotating flexible dipoles at the interface, independent of the properties in the hydrophobic region.}
}

@article{ando2001stable,
  title={A stable fluctuating-charge polarizable model for molecular dynamics simulations: Application to aqueous electron transfers},
  author={Ando, Koji},
  journal={The Journal of Chemical Physics},
  volume={115},
  number={11},
  pages={5228--5237},
  year={2001},
  publisher={American Institute of Physics}
}


@Article{Catte2016,
author ="Catte, Andrea and Girych, Mykhailo and Javanainen, Matti and Loison, Claire and Melcr, Josef and Miettinen, Markus S. and Monticelli, Luca and Määttä, Jukka and Oganesyan, Vasily S. and Ollila, O. H. Samuli and Tynkkynen, Joona and Vilov, Sergey",
title  ="Molecular electrometer and binding of cations to phospholipid bilayers",
journal  ="Phys. Chem. Chem. Phys.",
year  ="2016",
volume  ="18",
issue  ="47",
pages  ="32560-32569",
publisher  ="The Royal Society of Chemistry",
doi  ="10.1039/C6CP04883H",
url  ="http://dx.doi.org/10.1039/C6CP04883H",
abstract  ="Despite the vast amount of experimental and theoretical studies on the binding affinity of cations – especially the biologically relevant Na+ and Ca2+ – for phospholipid bilayers{,} there is no consensus in the literature. Here we show that by interpreting changes in the choline headgroup order parameters according to the ‘molecular electrometer’ concept [Seelig et al.{,} Biochemistry{,} 1987{,} 26{,} 7535]{,} one can directly compare the ion binding affinities between simulations and experiments. Our findings strongly support the view that in contrast to Ca2+ and other multivalent ions{,} Na+ and other monovalent ions (except Li+) do not specifically bind to phosphatidylcholine lipid bilayers at sub-molar concentrations. However{,} the Na+ binding affinity was overestimated by several molecular dynamics simulation models{,} resulting in artificially positively charged bilayers and exaggerated structural effects in the lipid headgroups. While qualitatively correct headgroup order parameter response was observed with Ca2+ binding in all the tested models{,} no model had sufficient quantitative accuracy to interpret the Ca2+:lipid stoichiometry or the induced atomistic resolution structural changes. All scientific contributions to this open collaboration work were made publicly{,} using nmrlipids.blogspot.fi as the main communication platform."}

@article{Chen2021,
author = {Chen, Peiran and Vorobyov, Igor and Roux, Benoît and Allen, Toby W.},
title = {Molecular Dynamics Simulations Based on Polarizable Models Show that Ion Permeation Interconverts between Different Mechanisms as a Function of Membrane Thickness},
journal = {The Journal of Physical Chemistry B},
volume = {125},
number = {4},
pages = {1020-1035},
year = {2021},
doi = {10.1021/acs.jpcb.0c08613},


URL = { 
        https://doi.org/10.1021/acs.jpcb.0c08613
    
},
eprint = { 
        https://doi.org/10.1021/acs.jpcb.0c08613
    
}

}

@article{Grossfield2003,
author = {Grossfield, Alan and Ren, Pengyu and Ponder, Jay W.},
title = {Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field},
journal = {Journal of the American Chemical Society},
volume = {125},
number = {50},
pages = {15671-15682},
year = {2003},
doi = {10.1021/ja037005r},
  

URL = { 
        https://doi.org/10.1021/ja037005r
    
},
eprint = { 
        https://doi.org/10.1021/ja037005r
    
}

}

@article{Han2018,
author = {Han, Kyungreem and Venable, Richard M. and Bryant, Anne-Marie and Legacy, Christopher J. and Shen, Rong and Li, Hui and Roux, Benoît and Gericke, Arne and Pastor, Richard W.},
title = {Graph–Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions},
journal = {The Journal of Physical Chemistry B},
volume = {122},
number = {4},
pages = {1484-1494},
year = {2018},
doi = {10.1021/acs.jpcb.7b10730},
    

URL = { 
        https://doi.org/10.1021/acs.jpcb.7b10730
    
},
eprint = { 
        https://doi.org/10.1021/acs.jpcb.7b10730
    
}

}

@article{inakollu2020polarisable,
  title={Polarisable force fields: what do they add in biomolecular simulations?},
  author={Inakollu, VS Sandeep and Geerke, Daan P and Rowley, Christopher N and Yu, Haibo},
  journal={Current Opinion in Structural Biology},
  volume={61},
  pages={182--190},
  year={2020},
  publisher={Elsevier}
}
@article{jing2019polarizable,
  title={Polarizable force fields for biomolecular simulations: Recent advances and applications},
  author={Jing, Zhifeng and Liu, Chengwen and Cheng, Sara Y and Qi, Rui and Walker, Brandon D and Piquemal, Jean-Philip and Ren, Pengyu},
  journal={Annual Review of biophysics},
  volume={48},
  pages={371},
  year={2019},
  publisher={NIH Public Access}
}
@article{baker2015polarizable,
  title={Polarizable force fields for molecular dynamics simulations of biomolecules},
  author={Baker, Christopher M},
  journal={Wiley Interdisciplinary Reviews: Computational Molecular Science},
  volume={5},
  number={2},
  pages={241--254},
  year={2015},
  publisher={Wiley Online Library}
}


@article{Databank,
 place={Cambridge}, title={NMRlipids Databank makes data-driven analysis of biomembrane properties accessible for all}, DOI={10.26434/chemrxiv-2023-jrpwm-v2}, journal={ChemRxiv}, publisher={Cambridge Open Engage}, author={Kiirikki, Anne and Antila, Hanne and Bort, Lara and Buslaev, Pavel and Fernando, Favela and Mendes Ferreira, Tiago and Fuchs, Patrick and Garcia-Fandino, Rebeca and Gushchin, Ivan and Kav, Batuhan and et al.}, year={2023}} This content is a preprint and has not been peer-reviewed.

@article{Klauda08,
title = {Rotation of Lipids in Membranes: Molecular Dynamics Simulation, 31P Spin-Lattice Relaxation, and Rigid-Body Dynamics},
journal = {Biophysical Journal},
volume = {94},
number = {8},
pages = {3074-3083},
year = {2008},
issn = {0006-3495},
doi = {https://doi.org/10.1529/biophysj.107.121806},
url = {https://www.sciencedirect.com/science/article/pii/S0006349508704648},
author = {Jeffery B. Klauda and Mary F. Roberts and Alfred G. Redfield and Bernard R. Brooks and Richard W. Pastor}
}

@article{kucerka2011,
title = {Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature},
journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes},
volume = {1808},
number = {11},
pages = {2761-2771},
year = {2011},
issn = {0005-2736},
doi = {https://doi.org/10.1016/j.bbamem.2011.07.022},
url = {https://www.sciencedirect.com/science/article/pii/S0005273611002276},
author = {Norbert Kučerka and Mu-Ping Nieh and John Katsaras},
keywords = {Area per lipid, Bilayer structure, Fluid phase, Neutron scattering, X-ray scattering, Phosphatidylcholine},
abstract = {The structural parameters of fluid phase bilayers composed of phosphatidylcholines with fully saturated, mixed, and branched fatty acid chains, at several temperatures, have been determined by simultaneously analyzing small-angle neutron and X-ray scattering data. Bilayer parameters, such as area per lipid and overall bilayer thickness have been obtained in conjunction with intrabilayer structural parameters (e.g. hydrocarbon region thickness). The results have allowed us to assess the effect of temperature and hydrocarbon chain composition on bilayer structure. For example, we found that for all lipids there is, not surprisingly, an increase in fatty acid chain trans–gauche isomerization with increasing temperature. Moreover, this increase in trans–gauche isomerization scales with fatty acid chain length in mixed chain lipids. However, in the case of lipids with saturated fatty acid chains, trans–gauche isomerization is increasingly tempered by attractive chain–chain van der Waals interactions with increasing chain length. Finally, our results confirm a strong dependence of lipid chain dynamics as a function of double bond position along fatty acid chains.}
}

@article{kucerka2008,
title = {Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data},
journal = {Biophysical Journal},
volume = {95},
number = {5},
pages = {2356-2367},
year = {2008},
issn = {0006-3495},
doi = {https://doi.org/10.1529/biophysj.108.132662},
url = {https://www.sciencedirect.com/science/article/pii/S0006349508783838},
author = {Norbert Kučerka and John F. Nagle and Jonathan N. Sachs and Scott E. Feller and Jeremy Pencer and Andrew Jackson and John Katsaras},
abstract = {Quantitative structures were obtained for the fully hydrated fluid phases of dioleoylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC) bilayers by simultaneously analyzing x-ray and neutron scattering data. The neutron data for DOPC included two solvent contrasts, 50% and 100% D2O. For DPPC, additional contrast data were obtained with deuterated analogs DPPC_d62, DPPC_d13, and DPPC_d9. For the analysis, we developed a model that is based on volume probability distributions and their spatial conservation. The model's design was guided and tested by a DOPC molecular dynamics simulation. The model consistently captures the salient features found in both electron and neutron scattering density profiles. A key result of the analysis is the molecular surface area, A. For DPPC at 50°C A=63.0Å2, whereas for DOPC at 30°C A=67.4Å2, with estimated uncertainties of 1Å2. Although A for DPPC agrees with a recently reported value obtained solely from the analysis of x-ray scattering data, A for DOPC is almost 10% smaller. This improved method for determining lipid areas helps to reconcile long-standing differences in the values of lipid areas obtained from stand-alone x-ray and neutron scattering experiments and poses new challenges for molecular dynamics simulations.}
}

@article{Lemkul2016,
author = {Lemkul, Justin A. and Huang, Jing and Roux, Benoît and MacKerell, Alexander D. Jr.},
title = {An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications},
journal = {Chemical Reviews},
volume = {116},
number = {9},
pages = {4983-5013},
year = {2016},
doi = {10.1021/acs.chemrev.5b00505},
  

URL = { 
        https://doi.org/10.1021/acs.chemrev.5b00505
    
},
eprint = { 
        https://doi.org/10.1021/acs.chemrev.5b00505
    
}

}

@article{lamoreux2003,
    author = {Lamoureux, Guillaume and Roux, Benoı̂t},
    title = "{Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm}",
    journal = {The Journal of Chemical Physics},
    volume = {119},
    number = {6},
    pages = {3025-3039},
    year = {2003},
    month = {07},
    abstract = "{A simple treatment for incorporating induced polarization in computer simulations is formulated on the basis of the classical Drude oscillator model. In this model, electronic induction is represented by the displacement of a charge-carrying massless particle attached to a polarizable atom under the influence of the local electric field. The traditional self-consistent field (SCF) regime of induced polarization is reproduced if these auxiliary particles are allowed to relax instantaneously to their local energy minima for any given fixed configuration of the atoms in the system. In practice, such treatment is computationally prohibitive for generating molecular dynamics trajectories because the electric field must be recalculated several times iteratively to satisfy the SCF condition, and it is important to seek a more efficient way to simulate the classical Drude oscillator model. It is demonstrated that a close approximation to the SCF regime can be simulated efficiently by considering the dynamics of an extended Lagrangian in which a small mass is attributed to the auxiliary particles, and the amplitude of their oscillations away from the local energy minimum is controlled with a low-temperature thermostat. A simulation algorithm in this modified two-temperature isobaric–isothermal ensemble is developed. The algorithm is tested and illustrated using a rigid three-site water model with one additional Drude particle attached to the oxygen which is closely related to the polarizable SPC model of Ahlström et al. [Mol. Phys. 68, 563 (1989)]. The tests with the extended Lagrangian show that stable and accurate molecular dynamics trajectories for large integration time steps (1 or 2 fs) can be generated and that liquid properties equivalent to SCF molecular dynamics can be reproduced at a fraction of the computational cost.}",
    issn = {0021-9606},
    doi = {10.1063/1.1589749},
    url = {https://doi.org/10.1063/1.1589749},
    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/119/6/3025/10853811/3025\_1\_online.pdf},
}

@article{Lynch21,
author = {Lynch, Charlotte I. and Klesse, Gianni and Rao, Shanlin and Tucker, Stephen J. and Sansom, Mark S. P.},
title = {Water Nanoconfined in a Hydrophobic Pore: Molecular Dynamics Simulations of Transmembrane Protein 175 and the Influence of Water Models},
journal = {ACS Nano},
volume = {15},
number = {12},
pages = {19098-19108},
year = {2021},
doi = {10.1021/acsnano.1c06443},
   

URL = { 
        https://doi.org/10.1021/acsnano.1c06443
    
},
eprint = { 
        https://doi.org/10.1021/acsnano.1c06443
    
}

}

@article{Ngo2019,
author = {Ngo, Van A. and Fanning, John Keenan and Noskov, Sergei Yu},
title = {Comparative Analysis of Protein Hydration from MD simulations with Additive and Polarizable Force Fields},
journal = {Advanced Theory and Simulations},
volume = {2},
number = {2},
pages = {1800106},
keywords = {conformational dynamics, hydrogen bonds, polarizable force fields, proteins, simulations},
doi = {https://doi.org/10.1002/adts.201800106},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adts.201800106},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/adts.201800106},
abstract = {Abstract Recent development of the Drude polarizable (Drude) force field (FF), based on the extension of an induced dipole model, has reached a milestone in the past few years providing a complete set of polarizable parameters for proteins, water, ions, and many lipid types. This FF enables stable simulations up to microseconds, surpassing the capability of other polarizable FFs. The quality of the Drude FF, however, has remained largely untested for modeling the secondary structures of small peptides in explicit solvents compared with classical non-polarizable FFs. It is critical to benchmark the complex and mutually dependent dynamics of hydrogen-bond (H-bond) networks formed by water–water, protein–water, and protein–protein interactions that are expected to have a major impact on the stability of protein structures and their conformational space. Here, a direct comparison is presented between the current Drude FF and the CHARMM-36 non-polarizable classical FF for 1) the solvation free energy of mimetics for all amino acid side-chain equivalents, 2) limited conformational space, 3) protein–water and protein–protein interactions, and 4) the comparative lifetimes of H-bonds. The impact of counterions on the stabilization of secondary structure in model peptides is additionally discussed and compared between these FFs.},
year = {2019}
}

@article{nochebuena23,
author = {Nochebuena, Jorge and Piquemal, Jean-Philip and Liu, Shubin and Cisneros, G. Andrés},
title = {Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-polarizable Force Fields},
journal = {Journal of Chemical Theory and Computation},
volume = {0},
number = {0},
pages = {null},
year = {0},
doi = {10.1021/acs.jctc.3c00762},
   

URL = { 
    
        https://doi.org/10.1021/acs.jctc.3c00762
    
    

},
eprint = { 
    
        https://doi.org/10.1021/acs.jctc.3c00762
    
    

}

}


@article{Ren2011polorganic,
author = {Ren, Pengyu and Wu, Chuanjie and Ponder, Jay W.},
title = {Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules},
journal = {Journal of Chemical Theory and Computation},
volume = {7},
number = {10},
pages = {3143-3161},
year = {2011},
doi = {10.1021/ct200304d},
   

URL = { 
        https://doi.org/10.1021/ct200304d
    
},
eprint = { 
        https://doi.org/10.1021/ct200304d
    
}

}




@Article{Rickeard2020,
author ="Rickeard, Brett W. and Nguyen, Michael H. L. and DiPasquale, Mitchell and Yip, Caesar G. and Baker, Hamilton and Heberle, Frederick A. and Zuo, Xiaobing and Kelley, Elizabeth G. and Nagao, Michihiro and Marquardt, Drew",
title  ="Transverse lipid organization dictates bending fluctuations in model plasma membranes",
journal  ="Nanoscale",
year  ="2020",
volume  ="12",
issue  ="3",
pages  ="1438-1447",
publisher  ="The Royal Society of Chemistry",
doi  ="10.1039/C9NR07977G",
url  ="http://dx.doi.org/10.1039/C9NR07977G",
abstract  ="Membrane undulations play a vital role in many biological processes{,} including the regulation of membrane protein activity. The asymmetric lipid composition of most biological membranes complicates theoretical description of these bending fluctuations{,} yet experimental data that would inform any such a theory is scarce. Here{,} we used neutron spin-echo (NSE) spectroscopy to measure the bending fluctuations of large unilamellar vesicles (LUV) having an asymmetric transbilayer distribution of high- and low-melting lipids. The asymmetric vesicles were prepared using cyclodextrin-mediated lipid exchange{,} and were composed of an outer leaflet enriched in egg sphingomyelin (ESM) and an inner leaflet enriched in 1-palmitoyl-2-oleoyl-phosphoethanolamine (POPE){,} which have main transition temperatures of 37 °C and 25 °C{,} respectively. The overall membrane bending rigidity was measured at three temperatures: 15 °C{,} where both lipids are in a gel state; 45 °C{,} where both lipids are in a fluid state; and 30 °C{,} where there is gel-fluid co-existence. Remarkably{,} the dynamics for the fluid asymmetric LUVs (aLUVs) at 30 °C and 45 °C do not follow trends predicted by their symmetric counterparts. At 30 °C{,} compositional asymmetry suppressed the bending fluctuations{,} with the asymmetric bilayer exhibiting a larger bending modulus than that of symmetric bilayers corresponding to either the outer or inner leaflet. We conclude that the compositional asymmetry and leaflet coupling influence the internal dissipation within the bilayer and result in membrane properties that cannot be directly predicted from corresponding symmetric bilayers."}

@article{Stone1981,
  title={Distributed multipole analysis, or how to describe a molecular charge distribution},
  author={Stone, Anthony J},
  journal={Chemical Physics Letters},
  volume={83},
  number={2},
  pages={233--239},
  year={1981},
  publisher={Elsevier}
}

@article{Tan2022,
author = {Tan, Qiaozhu and Ding, Ye and Qiu, Zongyang and Huang, Jing},
title = {Binding Energy and Free Energy of Calcium Ion to Calmodulin EF-Hands with the Drude Polarizable Force Field},
journal = {ACS Physical Chemistry Au},
volume = {2},
number = {2},
pages = {143-155},
year = {2022},
doi = {10.1021/acsphyschemau.1c00039},

URL = { 
        https://doi.org/10.1021/acsphyschemau.1c00039
},
eprint = { 
        https://doi.org/10.1021/acsphyschemau.1c00039   
}
}

@article{Thole1981,
title = {Molecular polarizabilities calculated with a modified dipole interaction},
journal = {Chemical Physics},
volume = {59},
number = {3},
pages = {341-350},
year = {1981},
issn = {0301-0104},
doi = {https://doi.org/10.1016/0301-0104(81)85176-2},
url = {https://www.sciencedirect.com/science/article/pii/0301010481851762},
author = {B.T. Thole},
abstract = {The point dipole interaction model for molecular polarizability recently proposed by Applequist, Carl, and Fung is modified by replacing the point dipole interaction by an interaction between smeared out dipoles. Rules are developed to indicate plausible forms for this modified interaction. The polarizabilities of a wide range of chemically different molecules can be calculated, using for each atom one polarizability independent of its chemical enviromnent. The errors are comparable to experimental uncertainty. Special care is taken to produce a model that tends to avoid infinite polarizabilities without use of cutoffs at short distances.}
}

@Article{kav2022,
author ="Kav, Batuhan and Strodel, Birgit",
title  ="Does the inclusion of electronic polarisability lead to a better modelling of peptide aggregation?",
journal  ="RSC Adv.",
year  ="2022",
volume  ="12",
issue  ="32",
pages  ="20829-20837",
publisher  ="The Royal Society of Chemistry",
doi  ="10.1039/D2RA01478E",
url  ="http://dx.doi.org/10.1039/D2RA01478E",
abstract  ="Simulating the process of amyloid aggregation with atomic detail is a challenging task for various reasons. One of them is that it is difficult to parametrise a force field such that all protein states ranging from the folded through the unfolded to the aggregated state are represented with the same level of accuracy. Here{,} we test whether the consideration of electronic polarisability improves the description of the different states of Aβ16–22. Surprisingly{,} the CHARMM Drude polarisable force field is found to perform worse than its unpolarisable counterpart CHARMM36m. Sources for this failure of the Drude model are discussed."}
@article{klesse2020induced,
  title={Induced polarization in molecular dynamics simulations of the 5-HT3 receptor channel},
  author={Klesse, Gianni and Rao, Shanlin and Tucker, Stephen J and Sansom, Mark SP},
  journal={Journal of the American Chemical Society},
  volume={142},
  number={20},
  pages={9415--9427},
  year={2020},
  publisher={ACS Publications}
}
@article{kognole2022charmm,
  title={CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field},
  author={Kognole, Abhishek A and Lee, Jumin and Park, Sang-Jun and Jo, Sunhwan and Chatterjee, Payal and Lemkul, Justin A and Huang, Jing and MacKerell Jr, Alexander D and Im, Wonpil},
  journal={Journal of computational chemistry},
  volume={43},
  number={5},
  pages={359--375},
  year={2022},
  publisher={Wiley Online Library}
}
@article{jo2008charmm,
  title={CHARMM-GUI: a web-based graphical user interface for CHARMM},
  author={Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G and Im, Wonpil},
  journal={Journal of computational chemistry},
  volume={29},
  number={11},
  pages={1859--1865},
  year={2008},
  publisher={Wiley Online Library}
}
@article{lee2016charmm,
  title={CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field},
  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 others},
  journal={Journal of chemical theory and computation},
  volume={12},
  number={1},
  pages={405--413},
  year={2016},
  publisher={ACS Publications}
}
@misc{wu2014charmm,
  title={CHARMM-GUI membrane builder toward realistic biological membrane simulations},
  author={Wu, Emilia L and Cheng, Xi and Jo, Sunhwan and Rui, Huan and Song, Kevin C and D{\'a}vila-Contreras, Eder M and Qi, Yifei and Lee, Jumin and Monje-Galvan, Viviana and Venable, Richard M and others},
  year={2014},
  publisher={Wiley Online Library}
}
@article{jo2009charmm,
  title={CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes},
  author={Jo, Sunhwan and Lim, Joseph B and Klauda, Jeffery B and Im, Wonpil},
  journal={Biophysical journal},
  volume={97},
  number={1},
  pages={50--58},
  year={2009},
  publisher={Elsevier}
}
@article{jo2007automated,
  title={Automated builder and database of protein/membrane complexes for molecular dynamics simulations},
  author={Jo, Sunhwan and Kim, Taehoon and Im, Wonpil},
  journal={PloS one},
  volume={2},
  number={9},
  pages={e880},
  year={2007},
  publisher={Public Library of Science San Francisco, USA}
}
@article{lee2018charmm,
  title={CHARMM-GUI membrane builder for complex biological membrane simulations with glycolipids and lipoglycans},
  author={Lee, Jumin and Patel, Dhilon S and St{\aa}hle, Jonas and Park, Sang-Jun and Kern, Nathan R and Kim, Seonghoon and Lee, Joonseong and Cheng, Xi and Valvano, Miguel A and Holst, Otto and others},
  journal={Journal of chemical theory and computation},
  volume={15},
  number={1},
  pages={775--786},
  year={2018},
  publisher={ACS Publications}
}
@article{wennberg2013lennard,
  title={Lennard-Jones lattice summation in bilayer simulations has critical effects on surface tension and lipid properties},
  author={Wennberg, Christian L and Murtola, Teemu and Hess, Berk and Lindahl, Erik},
  journal={Journal of chemical theory and computation},
  volume={9},
  number={8},
  pages={3527--3537},
  year={2013},
  publisher={ACS Publications}
}
@article{yu2023drude,
  title={Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids},
  author={Yu, Yalun and Venable, Richard M and Thirman, Jonathan and Chatterjee, Payal and Kumar, Anmol and Pastor, Richard W and Roux, Beno{\^\i}t and MacKerell Jr, Alexander D and Klauda, Jeffery B},
  journal={Journal of Chemical Theory and Computation},
  volume={19},
  number={9},
  pages={2590--2605},
  year={2023},
  publisher={ACS Publications}
}

@article{Yue2022,
title = {Ion permeation, selectivity, and electronic polarization in fluoride channels},
journal = {Biophysical Journal},
volume = {121},
number = {7},
pages = {1336-1347},
year = {2022},
issn = {0006-3495},
doi = {https://doi.org/10.1016/j.bpj.2022.02.019},
url = {https://www.sciencedirect.com/science/article/pii/S0006349522001436},
author = {Zhi Yue and Zhi Wang and Gregory A. Voth},
abstract = {Fluoride channels (Flucs) export toxic F− from the cytoplasm. Crystallography and mutagenesis have identified several conserved residues crucial for fluoride transport, but the permeation mechanism at the molecular level has remained elusive. Herein, we have applied constant-pH molecular dynamics and free-energy-sampling methods to investigate fluoride permeation through a Fluc protein from Escherichia coli. We find that fluoride is facile to permeate in its charged form, i.e., F−, by traversing through a non-bonded network. The extraordinary F− selectivity is gained by the hydrogen-bonding capability of the central binding site and the Coulombic filter at the channel entrance. The F− permeation rate calculated using an electronically polarizable force field is significantly more accurate compared with the experimental value than that calculated using a more standard additive force field, suggesting an essential role for electronic polarization in the F−–Fluc interactions.}
}

@article{Venable2013,
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 = {The Journal of Physical Chemistry B},
volume = {117},
number = {35},
pages = {10183-10192},
year = {2013},
doi = {10.1021/jp401512z},
 

URL = { 
        https://doi.org/10.1021/jp401512z
    
},
eprint = { 
        https://doi.org/10.1021/jp401512z
    
}

}



@article{brooks2009charmm,
  title={CHARMM: the biomolecular simulation program},
  author={Brooks, Bernard R and Brooks III, Charles L and Mackerell Jr, Alexander D and Nilsson, Lennart and Petrella, Robert J and Roux, Beno{\^\i}t and Won, Youngdo and Archontis, Georgios and Bartels, Christian and Boresch, Stefan and others},
  journal={Journal of computational chemistry},
  volume={30},
  number={10},
  pages={1545--1614},
  year={2009},
  publisher={Wiley Online Library}
}
@misc{drudegithub,
 title = {{Gromacs}},
 howpublished = "\url{https://github.com/gromacs/gromacs/tree/drude}"
 }
@misc{amoebagithub,
  title = {{OpenMM Scripts for AMOEBA Force Field MD Simulations}},
  howpublished = "\url{https://github.com/Inniag/openmm-scripts-amoeba}"
}
@article{eastman2017openmm,
  title={OpenMM 7: Rapid development of high performance algorithms for molecular dynamics},
  author={Eastman, Peter and Swails, Jason and Chodera, John D and McGibbon, Robert T and Zhao, Yutong and Beauchamp, Kyle A and Wang, Lee-Ping and Simmonett, Andrew C and Harrigan, Matthew P and Stern, Chaya D and others},
  journal={PLoS computational biology},
  volume={13},
  number={7},
  pages={e1005659},
  year={2017},
  publisher={Public Library of Science San Francisco, CA USA}
}
@dataset{richard_m_venable_2023_7871949,
  author       = {Richard M. Venable},
  title        = {{OpenMM  simulations of POPC using the CHARMM 
                   Drude2023 force field}},
  month        = apr,
  year         = 2023,
  note         = {{The data files contain additional atom types for 
                   the Drude particles and oxygen lone pairs}},
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7871949},
  url          = {https://doi.org/10.5281/zenodo.7871949}
}
@dataset{kav_batuhan_2023_7916287,
  author       = {Kav, Batuhan},
  title        = {{OpenMM simulations of POPC using the CHARMM 
                   Drude2023 force field in xtc format}},
  month        = may,
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7916287},
  url          = {https://doi.org/10.5281/zenodo.7916287}
}
@dataset{kav_batuhan_2021_7604627,
  author       = {Kav, Batuhan},
  title        = {{Pure POPE membrane simulations with the CHARMM- 
                   Drude force field (OpenMM 7.5.0)}},
  month        = apr,
  year         = 2021,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7604627},
  url          = {https://doi.org/10.5281/zenodo.7604627}
}
@dataset{kav_batuhan_2023_7916494,
  author       = {Kav, Batuhan},
  title        = {{OpenMM simulations of POPE using the CHARMM 
                   Drude2023 force field in xtc format}},
  month        = may,
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7916494},
  url          = {https://doi.org/10.5281/zenodo.7916494}
}
@dataset{kav_batuhan_2023_7622838,
  author       = {Kav, Batuhan},
  title        = {{MD Simulation data for a pure POPE bilayer with 
                   AMOEBA force field + OpenMM}},
  month        = feb,
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7622838},
  url          = {https://doi.org/10.5281/zenodo.7622838}
}
@article{antila2020quasi,
	title={Quasi-uncoupled rotational diffusion of phospholipid headgroups from the main molecular frame},
	author={Antila, Hanne S and Wurl, Anika and Ollila, OH and Miettinen, Markus S and Ferreira, Tiago M},
	journal={arXiv preprint arXiv:2009.06774},
	year={2020}
}
@dataset{kav_batuhan_2023_8000133,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC membrane simulations with 1000 mM NaCl 
                   with the CHARMM-Drude2023 force field (OpenMM)}},
  month        = jun,
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.8000133},
  url          = {https://doi.org/10.5281/zenodo.8000133}
}
@dataset{kav_batuhan_2023_8000095,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC membrane simulations with 350 mM NaCl 
                   with the CHARMM-Drude2023 force field (OpenMM)}},
  month        = jun,
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.8000095},
  url          = {https://doi.org/10.5281/zenodo.8000095}
}
@dataset{kav_batuhan_2023_8000065,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC membrane simulations with 350 mM CaCl2 
                   with the CHARMM-Drude2023 force field (OpenMM)}},
  month        = jun,
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.8000065},
  url          = {https://doi.org/10.5281/zenodo.8000065}
}
@dataset{kav_batuhan_2023_7992137,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC membrane simulations with 790 mM CaCl2 
                   with the CHARMM-Drude2023 force field (OpenMM)}},
  month        = may,
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7992137},
  url          = {https://doi.org/10.5281/zenodo.7992137}
}
@dataset{richard_m_venable_2023_7872447,
  author       = {Richard M. Venable},
  title        = {{OpenMM simulations of POPE using the CHARMM 
                   Drude2023 force field}},
  month        = apr,
  year         = 2023,
  note         = {{The data files contain additional atom types for 
                   the Drude particles and oxygen lone pairs}},
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7872447},
  url          = {https://doi.org/10.5281/zenodo.7872447}
}
@dataset{kav_batuhan_2021_7607436,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC membrane simulations with the CHARMM- 
                   Drude force field (OpenMM 7.5.0)}},
  month        = mar,
  year         = 2021,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7607436},
  url          = {https://doi.org/10.5281/zenodo.7607436}
}
@dataset{kav_batuhan_2020_7586915,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC Membrane with 350mM NaCl simulations 
                   using Drude Polarizable Force Field and OpenMM}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7586915},
  url          = {https://doi.org/10.5281/zenodo.7586915}
}
@dataset{kav_batuhan_2020_7591753,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC Membrane with 450mM NaCl simulations 
                   using Drude Polarizable Force Field and OpenMM}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7591753},
  url          = {https://doi.org/10.5281/zenodo.7591753}
}
@dataset{kav_batuhan_2020_7596011,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC Membrane with 650mM NaCl simulations 
                   using Drude Polarizable Force Field and OpenMM}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7596011},
  url          = {https://doi.org/10.5281/zenodo.7596011}
}
@dataset{kav_batuhan_2020_7600326,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC Membrane with 1000mM NaCl simulations 
                   using Drude Polarizable Force Field and OpenMM}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7600326},
  url          = {https://doi.org/10.5281/zenodo.7600326}
}
@dataset{kav_batuhan_2023_7658975,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC membrane simulations with 1000 mM CaCl2 
                   with the CHARMM-Drude force field (OpenMM)}},
  month        = mar,
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7658975},
  url          = {https://doi.org/10.5281/zenodo.7658975}
}
@dataset{kav_batuhan_2020_7600827,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC Membrane with 350mM CaCl2 simulations 
                   using Drude Polarizable Force Field and OpenMM}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7600827},
  url          = {https://doi.org/10.5281/zenodo.7600827}
}
@dataset{kav_batuhan_2020_7604040,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC Membrane with 650mM CaCl2 simulations 
                   using Drude Polarizable Force Field and OpenMM}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7604040},
  url          = {https://doi.org/10.5281/zenodo.7604040}
}
@dataset{kav_batuhan_2020_7605016,
  author       = {Kav, Batuhan},
  title        = {{Pure POPC Membrane with 450mM CaCl2 simulations 
                   using Drude Polarizable Force Field and OpenMM}},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7605016},
  url          = {https://doi.org/10.5281/zenodo.7605016}
}
@dataset{kav_batuhan_2022_7604681,
  author       = {Kav, Batuhan},
  title        = {{MD Simulation data for a pure DOPC bilayer without 
                   salt with AMOEBA force field + OpenMM}},
  month        = dec,
  year         = 2022,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7604681},
  url          = {https://doi.org/10.5281/zenodo.7604681}
}
@dataset{kav_batuhan_2022_7604711,
  author       = {Kav, Batuhan},
  title        = {{MD Simulation data for a pure DOPC bilayer (450 mM 
                   NaCl) with AMOEBA force field + OpenMM}},
  month        = dec,
  year         = 2022,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7604711},
  url          = {https://doi.org/10.5281/zenodo.7604711}
}
@dataset{kav_batuhan_2023_7625844,
  author       = {Kav, Batuhan},
  title        = {{MD Simulation data for a pure DOPC bilayer (1000 
                   mM NaCl) with AMOEBA force field + OpenMM}},
  month        = feb,
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7625844},
  url          = {https://doi.org/10.5281/zenodo.7625844}
}
@dataset{kav_batuhan_2022_7604842,
  author       = {Kav, Batuhan},
  title        = {{MD Simulation data for a pure DOPC bilayer (450 mM 
                   CaCl2) with AMOEBA force field + OpenMM}},
  month        = dec,
  year         = 2022,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7604842},
  url          = {https://doi.org/10.5281/zenodo.7604842}
}
@dataset{kav_batuhan_2022_7604810,
  author       = {Kav, Batuhan},
  title        = {{MD Simulation data for a pure DOPC bilayer (1000 
                   mM CaCl2) with AMOEBA force field + OpenMM}},
  month        = dec,
  year         = 2022,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7604810},
  url          = {https://doi.org/10.5281/zenodo.7604810}
}

@article{prajapati2020computational,
  title={Computational modeling of ion transport in bulk and through a nanopore using the drude polarizable force field},
  author={Prajapati, Jigneshkumar Dahyabhai and Mele, Crystal and Aksoyoglu, Mehmet Alphan and Winterhalter, Mathias and Kleinekath{\"o}fer, Ulrich},
  journal={Journal of Chemical Information and Modeling},
  volume={60},
  number={6},
  pages={3188--3203},
  year={2020},
  publisher={ACS Publications}
}

@article{shayestehpour2022ion,
  title={Ion Correlation in Choline Chloride--Urea Deep Eutectic Solvent (Reline) from Polarizable Molecular Dynamics Simulations},
  author={Shayestehpour, Omid and Zahn, Stefan},
  journal={The Journal of Physical Chemistry B},
  volume={126},
  number={18},
  pages={3439--3449},
  year={2022},
  publisher={ACS Publications}
}

@article{ponder2010current,
  title={Current status of the AMOEBA polarizable force field},
  author={Ponder, Jay W and Wu, Chuanjie and Ren, Pengyu and Pande, Vijay S and Chodera, John D and Schnieders, Michael J and Haque, Imran and Mobley, David L and Lambrecht, Daniel S and DiStasio Jr, Robert A and others},
  journal={The journal of physical chemistry B},
  volume={114},
  number={8},
  pages={2549--2564},
  year={2010},
  publisher={ACS Publications}
}

@article{patel2004charmm,
  title={CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations},
  author={Patel, Sandeep and Brooks III, Charles L},
  journal={Journal of computational chemistry},
  volume={25},
  number={1},
  pages={1--16},
  year={2004},
  publisher={Wiley Online Library}
}

@dataset{ollila_2015_32498,
  author       = {Ollila, Samuli},
  title        = {{MD simulation trajectory and related files for 
                   POPC bilayer with 950mM NaCl (CHARMM36, Gromacs
                   4.5)}},
  month        = oct,
  year         = 2015,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.32498},
  url          = {https://doi.org/10.5281/zenodo.32498}
}

@dataset{ollila_2015_32497,
  author       = {Ollila, Samuli},
  title        = {{MD simulation trajectory and related files for 
                   POPC bilayer with 690mM NaCl (CHARMM36, Gromacs
                   4.5)}},
  month        = oct,
  year         = 2015,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.32497},
  url          = {https://doi.org/10.5281/zenodo.32497}
}

@dataset{ollila_2015_32496,
  author       = {Ollila, Samuli},
  title        = {{MD simulation trajectory and related files for 
                   POPC bilayer with 350mM NaCl (CHARMM36, Gromacs
                   4.5)}},
  month        = oct,
  year         = 2015,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.32496},
  url          = {https://doi.org/10.5281/zenodo.32496}
}

@dataset{nencini_ricky_2019_3434396,
  author       = {Nencini, Ricky},
  title        = {{CHARMM36, NB-Fix approaches, without NBFIX, POPC 
                   membrane, Ca, Na ions,}},
  month        = sep,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3434396},
  url          = {https://doi.org/10.5281/zenodo.3434396}
}

@dataset{melcr_josef_2017_3335503,
  author       = {Melcr, Josef},
  title        = {{Simulations of POPC lipid bilayer in water 
                   solution at various NaCl, KCl and CaCl2
                   concentrations using ECC-POPC force field}},
  month        = dec,
  year         = 2017,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3335503},
  url          = {https://doi.org/10.5281/zenodo.3335503}
}
@article{lin2018polarizable,
  title={Polarizable force field for molecular ions based on the classical Drude oscillator},
  author={Lin, Fang-Yu and Lopes, Pedro EM and Harder, Edward and Roux, Beno{\^\i}t and MacKerell Jr, Alexander D},
  journal={Journal of chemical information and modeling},
  volume={58},
  number={5},
  pages={993--1004},
  year={2018},
  publisher={ACS Publications}
}
@article{lamoureux2006polarizable,
  title={A polarizable model of water for molecular dynamics simulations of biomolecules},
  author={Lamoureux, Guillaume and Harder, Edward and Vorobyov, Igor V and Roux, Beno{\^\i}t and MacKerell Jr, Alexander D},
  journal={Chemical Physics Letters},
  volume={418},
  number={1-3},
  pages={245--249},
  year={2006},
  publisher={Elsevier}
}
@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},
  journal={SoftwareX},
  volume={1},
  pages={19--25},
  year={2015},
  publisher={Elsevier}
}
@article{phillips2020scalable,
  title={Scalable molecular dynamics on CPU and GPU architectures with NAMD},
  author={Phillips, James C and Hardy, David J and Maia, Julio DC and Stone, John E and Ribeiro, Jo{\~a}o V and Bernardi, Rafael C and Buch, Ronak and Fiorin, Giacomo and H{\'e}nin, J{\'e}r{\^o}me and Jiang, Wei and others},
  journal={The Journal of chemical physics},
  volume={153},
  number={4},
  year={2020},
  publisher={AIP Publishing}
}
@article{michaud2011mdanalysis,
  title={MDAnalysis: a toolkit for the analysis of molecular dynamics simulations},
  author={Michaud-Agrawal, Naveen and Denning, Elizabeth J and Woolf, Thomas B and Beckstein, Oliver},
  journal={Journal of computational chemistry},
  volume={32},
  number={10},
  pages={2319--2327},
  year={2011},
  publisher={Wiley Online Library}
}
@inproceedings{gowers2016mdanalysis,
  title={MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations},
  author={Gowers, Richard J and Linke, Max and Barnoud, Jonathan and Reddy, Tyler JE and Melo, Manuel N and Seyler, Sean L and Domanski, Jan and Dotson, David L and Buchoux, S{\'e}bastien and Kenney, Ian M and others},
  booktitle={Proceedings of the 15th python in science conference},
  volume={98},
  pages={105},
  year={2016},
  organization={SciPy Austin, TX}
}
@Article{         harris2020array,
 title         = {Array programming with {NumPy}},
 author        = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J.
                 van der Walt and Ralf Gommers and Pauli Virtanen and David
                 Cournapeau and Eric Wieser and Julian Taylor and Sebastian
                 Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
                 and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
                 Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del
                 R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre
                 G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and
                 Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
                 Travis E. Oliphant},
 year          = {2020},
 month         = sep,
 journal       = {Nature},
 volume        = {585},
 number        = {7825},
 pages         = {357--362},
 doi           = {10.1038/s41586-020-2649-2},
 publisher     = {Springer Science and Business Media {LLC}},
 url           = {https://doi.org/10.1038/s41586-020-2649-2}
}