@STRING{CELL="Cell"}
@STRING{JMB="J. Mol. Biol."}
@STRING{BIOCHEMISTRY="Biochemistry"}
@STRING{BIOPHYSICALCHEMISTRY="Biophys. Chem."}
@STRING{JCP="J. Chem. Phys."}
@STRING{PNAS="Proc. Natl. Acad. Sci. USA"}
@STRING{BIOPOLYMERS="Biopolymers"}
@STRING{SCIENCE="Science"}
@STRING{MMBR="Microbiol. Mol. Biol. R."}
@STRING{NATURE="Nature"}
@STRING{NATSTRUCTBIOL="Nat. Struct. Biol."}
@STRING{NATBIOTECHNOL="Nat. Biotechnol."}
@STRING{JBIOLCHEM="J. Biol. Chem."}
@STRING{JSTRUCTBIOL="J. Struct. Biol."}
@STRING{FOLDINGANDDESIGN="Folding and Design"}
%@STRING{PROTSTRFUNCGEN="Prot. Str. Func. Gen."}
@STRING{PROTSTRFUNCGEN="Proteins"}
@STRING{PRL="Phys. Rev. Lett."}
@STRING{TIBS="Trends in Biochem. Sci."}
@STRING{EMBOJ="EMBO J."}
@STRING{FEBS="FEBS Letters"}
@STRING{FASEB="FASEB"}
@STRING{JBIOCHEMTOXICOL="J. Biochem. Toxicol."}
@STRING{CRBMB="Crit. Rev. Biochem. Mol. Biol."}
@STRING{CHEMREV="Chem. Rev."}
@STRING{ANNUREVBIOCHEM="Annu. Rev. Biochem."}
% ------------------  books ----------------------


@INBOOK{vanKampenBook,
   AUTHOR="van Kampen, N. G.",
   TITLE="Stochastic Processes in Physics and Chemistry, 2nd Edition",
   PUBLISHER="North Holland",
   PAGES={96--127},
   MONTH="July",
   DAY="1",
   YEAR=2001
}


@ARTICLE{LAMMPS,
   AUTHOR="S. Plimpton", 
   TITLE="Fast Parallel Algorithms for Short-Range Molecular Dynamics", 
   JOURNAL="J. Comp. Phys.", 
   VOLUME=117,
   PAGES={1--19},
   YEAR="1995",
   NOTE={\url{http://lammps.sandia.gov/}}
}


@ARTICLE{packmol,
  AUTHOR="Martínez, L. and Andrade, R. and Brigin, E. G. and Martínez, J. M.",
  TITLE="Packmol: A package for building initial configurations for molecular dynamics simulations.",
  JOURNAL="J. Comp. Chem.",
  VOLUME=30,
  NUMBER=13,
  PAGES={2157--2164},
  YEAR=2009,
  NOTE={\url{http://www.ime.unicamp.br/~martinez/packmol/}}
}


%% The primary VMD citation, should be used by all publications using VMD
@article{VMD,
  author={William Humphrey and Andrew Dalke and Klaus Schulten},
  title={{VMD} -- {V}isual {M}olecular {D}ynamics},
  journal={Journal of Molecular Graphics},
  year=1996,
  volume=14,
  pages={33-38},
  tbstatus={Published.},
  techrep={},
  tbreference={222},
  NOTE={\url{http://www.ks.uiuc.edu/Research/vmd}}
}

%% Interactive Molecular Dynamics, cited by papers doing IMD simulations
@inproceedings{VMDIMD,
  author={John Stone and Justin Gullingsrud and Paul Grayson and Klaus Schulten},
  title={A System for Interactive Molecular Dynamics Simulation},
  booktitle={2001 ACM Symposium on Interactive 3D Graphics},
  publisher={ACM SIGGRAPH},
  address={New York},
  editor={John F. Hughes and Carlo H. S\'equin},
  pages={191-194},
  year={2001},
  note={},
  tbreference={304},
  tbstatus={Published.},
  annote={This symposium took place between March 19-21, 2001. {ISBN} 1-58113-292-1.}
}


@ARTICLE{MOLTEMPLATE,
   AUTHOR="A.I. Jewett and D. Stelter and J. Lambert and S.M. Saladi and O.M. Roscioni and M. Ricci and L. Autin and M. Maritan and S.M. Bashusqeh and T. Keyes and R.T. Dame and J.-E. Shea and G.J. Jensen and D.S. Goodsell", 
   TITLE="Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics",
   JOURNAL="J. Mol. Biol.",
   VOLUME=433,
   NUMBER=11,
   PAGES=166841,
   YEAR="2021",
   NOTE={\url{https://doi.org/10.1016/j.jmb.2021.166841}}
}


@MISC{topotools,
  AUTHOR="Axel Kohlmeyer",
  TITLE="{The TopoTools VMD plugin}",
  HOWPUBLISHED={\url{http://sites.google.com/site/akohlmey/software/topotools/}}
}


@MISC{pizzapy,
  AUTHOR="Steve Plimpton",
  TITLE="{The Pizza.py toolkit}",
  HOWPUBLISHED={\url{http://www.cs.sandia.gov/~sjplimp/pizza.html}}
}


@ARTICLE{TraPPE,
  AUTHOR="Marcus G. Martin and J. Ilja Siepmann",
  TITLE="Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes",
  JOURNAL="J. Phys. Chem. B",
  VOLUME=102,
  NUMBER=14,
  PAGES={2569--2577},
  YEAR=1998
}


@ARTICLE{OpenBABEL,
  AUTHOR="N.M. O'Boyle and M.Banck and C.A. James and C. Morley and T. Vandermeersch and G.R. Hutchison",
  TITLE="Open Babel: An open chemical toolbox",
  JOURNAL="J. Cheminf.",
  VOLUME=3,
  NUMBER=33,
  YEAR=2011
}


@ARTICLE{ATB,
  AUTHOR="A.K. Malde and L. Zuo and M. Breeze and M. Stroet and D. Poger and P.C. Nair and C. Oostenbrink and A.E. Mark",
  TITLE="An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0",
  JOURNAL="J. Chem. Theory Comput.",
  VOLUME=7,
  PAGES={4026--4037},
  YEAR=2011
}


@ARTICLE{OVITO,
  AUTHOR="Alexander Stukowski",
  TITLE="Modelling and Simulation in Materials Science and Engineering Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool",
  JOURNAL="Modelling Simul. Mater. Sci. Eng.",
  VOLUME=18,
  YEAR=2010
}


@ARTICLE{Raviv++SafinyaBiophysJ2007,
   AUTHOR="Uri Raviv and Toan Nguyen and Rouzbeh Ghafouri and Daniel J. Needleman and Youli Li and Herbert P. Miller and Leslie Wilson and Robijn F. Bruinsma and Cyrus R. Safinya",
   TITLE="Microtubule Protofilament Number Is Modulated in a Stepwise Fashion by the Charge Density of an Enveloping Layer",
   JOURNAL="Biophys. J.",
   VOLUME=92,
   NUMBER=1,
   PAGES={278--287},
   YEAR="2007",
   MONTH={January},
   DAY={1}
}


@ARTICLE{Raviv++SafinyaPNAS2005,
   AUTHOR="Uri Raviv and Daniel J. Needleman and Youli Li and Herbert P. Miller and Leslie Wilson and Cyrus R. Safinya",
   TITLE="Cationic liposome-microtubule complexes: Pathways to the formation of two-state lipid-protein nanotubes with open or closed ends",
   JOURNAL="Proc. Natl. Acad. Sci. USA",
   VOLUME=102,
   NUMBER=32,
   PAGES={11167--11172},
   YEAR="2005",
   MONTH={August},
   DAY={9}
}

@ARTICLE{Berendsen++StraatsmaJPhysChem1987,
   AUTHOR="H. J. C. Berendsen and J. R. Grigera and T. P. Straatsma",
   TITLE="The Missing Term in Effective Pair Potentials",
   JOURNAL="J. Phys. Chem.",
   VOLUME=91,
   NUMBER=24,
   PAGES={6269--6271},
   YEAR="1987",
}


@ARTICLE{Klimov+ThirumalaiPRL1997,
   AUTHOR="Klimov, D. K. and Thirumalai, D.",
   JOURNAL="Phys. Rev. Lett.",
   VOLUME=79,
   PAGES={317--320},
   YEAR="1997"
}
