Merge branch release-5-1

[gromacs.git] / docs / manual / monster.bib

@String{BTacr   = "Acc. Chem. Res."}
@String{BTacb   = "Act. Cryst. B."}
@String{BTacd   = "Act. Cryst. D."}
@String{BTacp   = "Adv. Chem. Phys."}
@String{BTang   = "Angew. Chemie"}
@String{BTarbb  = "Annu. Rev. Biophys. Biomol. Struct."}
@String{BTarbbc = "Annu. Rev. Biophys. Biophys. Chem."}
@String{BTarbc  = "Annu. Rev. Biochem."}
@String{BTarbp  = "Annu. Rev. Biophys."}
@String{BTarpc  = "Annu. Rev. Phys. Chem."}
@String{BTarp   = "Annu. Rev. Physiol."}
@String{BTarchbb= "Arch. Bioch. Bioph."}
@String{BTbba   = "Biochim. Biophys. Acta"}
@String{BTbcb   = "Biochem. Cell. Biol."}
@String{BTbbpc  = "Ber. Bunsenges. Phys. Chem."}
@String{BTbbrc  = "Biochem. Biophys. Res. Comm."}
@String{BTbioch = "Biochemistry"}
@String{BTbiopc = "Bioph. Chem."}
@String{BTbj    = "Biophys. J."}
@String{BTbiop  = "Biopolymers"}
@String{BTbi    = "Bioch. Int."}
@String{BTbmbi  = "Biochem. Mol. Biol. Int."}
@String{BTcb    = "Curr. Biol."}
@String{BTcosb  = "Curr. Opin. Struct. Biol."}
@String{BTcpc   = "Comp. Phys. Comm."}
@String{BTcpl   = "Chem. Phys. Lett."}
@String{BTcp    = "Chem. Phys."}
@String{BTcr    = "Chem. Rev."}
@String{BTcsr   = "Chem. Soc. Rev."}
@String{BTejb   = "Eur. J. Biochem."}
@String{BTebj   = "Eur. Biophys. J."}
@String{BTfaseb = "FASEB J."}
@String{BTfebs  = "FEBS Lett."}
@String{BTijqc  = "Int. J. Quant. Chem."}
@String{BTijpp  = "Int. J. Pept. Prot. Res."}
@String{BTisrjc = "Isr. J. Chem."}
@String{BTjacs  = "J. Am. Chem. Soc."}
@String{BTjapl  = "J. Appl. Crystallogr."}
@String{BTjaplp = "J. Appl. Phys."}
@String{BTjbc   = "J. Biol. Chem."}
@String{BTjbnmr = "J. Biomol. NMR"}
@String{BTjbsd  = "J. Biomol. Struct. Dyn."}
@String{BTjcaid = "J. Comp. Aid. Mol. Design"}
@String{BTjcc   = "J. Comp. Chem."}
@String{BTjced  = "J. Chem. Eng. Data"}
@String{BTjcomp = "J. Comp. Phys."}
@String{BTjcp   = "J. Chem. Phys."}
@String{BTjcsft = "J. Chem. Soc. Far. Trans."}
@String{BTjctc  = "J. Chem. Theory Comput."}
@String{BTjmb   = "J. Mol. Biol."}
@String{BTjmag  = "J. Magn. Reson."}
@String{BTjmagb = "J. Magn. Reson. Ser. B"}
@String{BTjmm   = "J. Mol. Mod."}
@String{BTjmst  = "J. Mol. Struct. (THEOCHEM)"}
@String{BTjms   = "J. Mol. Struct."}
@String{BTjpa   = "J. Phys. A."}
@String{BTjpc   = "J. Phys. Chem."}
@String{BTjpca  = "J. Phys. Chem. A."}
@String{BTjpcb  = "J. Phys. Chem. B."}
@String{BTlang  = "Langmuir"}
@String{BTmph   = "Mol. Phys."}
@String{BTmcb   = "Mol. Cell. Bioch."}
@string{BTmie   = "Methods in Enyzmology"}
@String{BTmsim  = "Mol. Sim."}
@String{BTnature= "Nature"}
@String{BTnsb   = "Nature Struct. Biol."}
@String{BTpeng  = "Prot. Eng."}
@String{BTpnas  = "Proc. Natl. Acad. Sci. USA"}
@String{BTpr    = "Phys. Rev."}
@String{BTpra   = "Phys. Rev. {\bf A}"}
@String{BTprb   = "Phys. Rev. {\bf B}"}
@String{BTpre   = "Phys. Rev. {\bf E}"}
@String{BTprl   = "Phys. Rev. Lett."}
@String{BTprot  = "PROTEINS: Struct. Funct. Gen."}
@String{BTpsci  = "Prot. Sci."}
@String{BTsci   = "Science"}
@String{BTstr   = "Structure"}
@String{BTtchim = "Theor. Chim. Acta."}
@String{BTtibs  = "Trends Biochem. Sci."}
@String{BTtibtech= "Trends Biotech."}

@Article{AWang95,
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  title =        {Reparametrization of the {K}arplus Relation for
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@Article{Aalten95,
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@Article{Ahlstrom89,
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@Article{Abad87,
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@Book{Abragam61,
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@Article{Adams79,
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@Article{Agmon96,
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@Article{Zhu97a,
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@Article{Byrd95a,
  author =       {R. H. Byrd and P. Lu and J. Nocedal},
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@Article{Alexandrov93,
  author =       "Nickolai Alexandrov",
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  year =         "1993",
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@Book{Allen87,
  author =       "M. P. Allen and D. J. Tildesley",
  title =        "Computer Simulations of Liquids",
  publisher =    "Oxford Science Publications",
  address =      "Oxford",
  year =         "1987",
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@Article{Astrand91,
  author =       "P. -O. {{\AA}}strand and A. Wallqvist and G.
                 Karlstr{\"o}m and P. Linse",
  title =        "Properties of urea-water solvation calculated from a
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  year =         "1991",
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@Article{Astrand94a,
  author =       "P. -O. {{\AA}}strand and A. Wallqvist and G.
                 Karlstr{\"o}m",
  title =        "Non-empirical potentials for Urea-Water systems",
  journal =      BTjcp,
  year =         "1994",
  volume =       "100",
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@Article{Astrand94b,
  author =       "P. -O. {{\AA}}strand and A. Wallqvist and G.
                 Karlstr{\"o}m",
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  journal =      BTjpc,
  year =         "1994",
  volume =       "98",
  pages =        "8224--8233",
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@Article{Alley83,
  author =       {W. E. Alley and B. J. Alder and S. Yip},
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@Article{Allinger76,
  author =       "N. L. Allinger \and J. Kao",
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@Article{Alper89,
  author =       {H. E. Alper and R. M. Levy},
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  year =         1989,
  volume =       91,
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@Article{Amadei93,
  author =       "Andrea Amadei and Antonius B. M. Linssen and Herman J.
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  title =        "Essential Dynamics of Proteins",
  journal =      BTprot,
  year =         "1993",
  volume =       "17",
  pages =        "412--425",
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@Article{Amadei96,
  author =       {A. Amadei and A. B. M. Linssen and B. L. de Groot and
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@Article{Andersen80,
  author =       {H. C. Andersen},
  title =        {Molecular dynamics simulations at constant pressure and/or temperature},
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  year =         1980,
  volume =       72,
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@Article{Anderson87,
  author =       {J. Anderson and J. J. Ullo and S. Yip},
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  volume =       87,
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@Article{Anfinsen73,
  author =       "Christian B. Anfinsen",
  title =        "Principles that Govern the Folding of Protein Chains",
  journal =      BTsci,
  year =         "1973",
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@Article{Angel83,
  author =       {C. A. Angell},
  title =        {Supercooled Water},
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@Article{Aqvist93,
  author =       "J. {{\AA}}qvist and A. Warshel",
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@Book{Arfken70,
  author =       {G. Arfken},
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@book{Atkins90,
  author =       {P. W. Atkins},
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@Article{Auffinger95a,
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@Article{Axelsen91,
  author =       {P. H. Axelsen and E. Gratton and F. G. Prendergast},
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@Article{BBrooks83,
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@Article{BBrooks83b,
  author =       {B. Brooks and M. Karplus},
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  volume =       80,
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@Article{Babu88,
  author =       "Y. Sudhakar Babu and Charles E. Bugg and William J.
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  title =        "Structure of Calmodulin Refined at 2.2{{\AA}}",
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  year =         "1988",
  volume =       "204",
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@Article{Bacon88,
  author =       "D. J. Bacon and W. F. Anderson",
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@Article{Baez94,
  author =       {L. A. B{\'a}ez and P. Clancy},
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@Article{Baker92,
  author =       "P. J. Baker and K. L. Britton and D. W. Rice and A.
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  year =         "1992",
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@InCollection{Bala92,
  author =       "P. Bala and B. Lesyng and T. N. Truong and J. A.
                 McCammon",
  booktitle =    "Molecular Aspects of Biotechnology: Computational
                 Models and Theories",
  title =        "Ab Initio Studies and Quantum-Classical Molecular
                 Dynamics Simulations for Proton Transfer Processes in
                 Model Systems and in Enzymes",
  publisher =    "Kluwer",
  year =         "1992",
  editor =       "J. Bertran",
  pages =        "299--326",
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@Article{Bala94,
  author =       "P. Bala and B. Lesyng and J. A. McCammon",
  title =        "Applications of Quantum-Classical and
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  year =         "1994",
  volume =       "180",
  pages =        "271--285",
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@Article{Baldwin95,
  author =       "R. L. Baldwin",
  title =        "The nature of protein folding pathways: The classical
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  year =         "1995",
  volume =       "5",
  pages =        "103--109",
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@Article{Baldwin96a,
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  title =        {Why is Protein Folding so Fast ?},
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  volume =       93,
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@Article{Balsera96,
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  volume =       100,
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@Article{Ban94,
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  title =        "Crystal structure of recombinant {P}aramecium
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  year =         "1994",
  volume =       "50",
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@Article{Banci92,
  author =       {L. Banci and I. Bertini and P. Carloni and
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  title =        {Molecular Dynamics Simulations on {HiPIP} from {\em
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  year =         1992,
  volume =       114,
  pages =        {10683--10689}
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@Article{Bancroft67,
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@Article{Barbato92,
  author =       "G. Barbato and M. Ikura and L. E. Kay and R. W. Pastor
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  title =        "Backbone Dynamics of Calmodulin Studied by {$^{15}$N}
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  journal =      BTbioch,
  year =         "1992",
  volume =       "31",
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@Article{Barth95a,
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@Article{Barthel90,
  author =       "J. Barthel and K. Bachhuber and R. Buchner and
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  year =         "1990",
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  OPTnumber =    "4",
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  OPTmonth =     "",
  OPTremark =    "Water, 25 C. 
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@Article{Basu94,
  author =       "Gautam Basu and Akio Kitao and Fumio Hirata and
                 Nobuhiro G{$\bar{\rm o}$}",
  title =        "A Collective Motion Description of the
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@Article{Bayley69,
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@Article{Bayley92,
  author =       "P. M. Bayley and S. R. Martin",
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  year =         "1992",
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@Article{Becke93,
  author =       "A. D. Becke",
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  year =         "1993",
  volume =       "98",
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@MastersThesis{Bekker87,
  author =       "H. Bekker",
  title =        "Ontwerp van een special-purpose computer voor
                 Moleculaire Dynamica Simulaties",
  school =       "RuG",
  year =         "1987",
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@InCollection{Bekker92,
  author =       "H. Bekker and E. J. Dijkstra and H. J. C. Berendsen",
  booktitle =    "Parallel Computing: From Theory to Sound Practice",
  title =        "Mapping molecular dynamics simulation calculations on
                 a ring architecture",
  publisher =    "IOS Press",
  pages =        "268--279",
  editor =       "P. T. Wu and E. Milgrom",
  year =         "1992",
  address =      "Amsterdam",
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@InProceedings{Bekker93a,
  author =       "H. Bekker and H. J. C. Berendsen and E. J. Dijkstra
                 and S. Achterop and R. van Drunen and D. van der Spoel
                 and A. Sij\-bers and H. Keegstra and B. Reitsma and M.
                 K. R. Renardus",
  title =        "Gromacs: {A} Parallel Computer for Molecular Dynamics
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  editor =       "R. A. de Groot and J. Nadrchal",
  pages =        "252--256",
  booktitle =    "Physics Computing 92",
  year =         "1993",
  publisher =    "World Scientific",
  address =      "Singapore",
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@Article{Brunne93,
  author =       "R. M. Brunne and W. F. van Gunsteren and R.
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  title =        "Molecular Dynamics simulation of the proline
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  journal =      BTjacs,
  year =         "1993",
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@Article{Bundi79,
  author =       "A. Bundi and K. W{\"u}thrich",
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@InProceedings{Bekker93b,
  author =       "H. Bekker and H. J. C. Berendsen and E. J. Dijkstra
                 and S. Achterop and R. v. Drunen and D. v. d. Spoel and
                 A. Sij\-bers and H. Keegstra and B. Reitsma and M. K.
                 R. Renardus",
  title =        {{Gromacs Method of Virial Calculation Using a Single
                 Sum}},
  editor =       "R. A. de Groot and J. Nadrchal",
  pages =        "257--261",
  booktitle =    "Physics Computing 92",
  year =         "1993",
  publisher =    "World Scientific",
  address =      "Singapore",
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@Article{Bekker95,
  author =       {H. Bekker and E. J. Dijkstra and M. K. R. Renardus and H. J. C. Berendsen},
  title =        {An Efficient, Box Shape Independent Non-Bonded Force and Virial  
          Algorithm for Molecular Dynamics},
  journal =      BTmsim,
  year =         1995,
  volume =       14,
  pages =        {137--152}
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@Article{Bera94,
  author =       "Aloke Kumar Bera and Biswadip Das and Subrata
                 Chattapahyay and Chanchal Dasgupta",
  title =        "Refolding of Denatured Restriction Endonucleases with
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  journal =      BTbbrc,
  year =         "1994",
  volume =       "32",
  pages =        "315--323",
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@InCollection{Berendsen81,
  author =       "H. J. C. Berendsen and J. P. M. Postma and W. F. van
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  booktitle =    "Intermolecular Forces",
  title =        "Interaction Models for Water in Relation to Protein
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  journal =      BTjcp,
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@InCollection{Berendsen84b,
  author =       {H. J. C. Berendsen and W. F. van Gunsteren},
  title =        {Molecular Dynamics Simulations: Techniques and Approaches},
  booktitle =    {Molecular Liquids-Dynamics and Interactions},
  publisher =    {Reidel},
  year =         1984,
  address =      {Dordrecht, The Netherlands},
  editor =       {A. J. Barnes et al.},
  series =       {NATO ASI C 135},
  pages =        {475--500}
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@Proceedings{Berendsen86a,
  title =        "Molecular-Dynamics Simulations of
                 Statistical-Mechanical Systems",
  year =         "1986",
  editor =       "G. Ciccotti and W. G. Hoover",
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  organization = "Internat. School of Physics Enrico Fermi",
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@InProceedings{Berendsen86b,
  author =       "H. J. C. Berendsen and W. F. van Gunsteren",
  title =        "Practical Algorithms for Dynamics Simulations",
  year =         "1986",
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@Article{Berendsen87,
  author =       "H. J. C. Berendsen and J. R. Grigera and T. P.
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@InCollection{Berendsen91,
  author =       "H. J. C. Berendsen",
  booktitle =    "Computer Simulations in Material Science",
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  publisher =    "Kluwer",
  year =         "1991",
  editor =       "M. Meyer and V. Pontikis",
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@InCollection{Berendsen93a,
  author =       "H. J. C. Berendsen",
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  title =        "Electrostatic interactions",
  publisher =    "ESCOM",
  year =         "1993",
  editor =       "W. F. van Gunsteren and P. K. Weiner and A. J.
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  pages =        "161--181",
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@Article{Berendsen93b,
  author =       "H. J. C. Berendsen and J. Mavri",
  title =        "Quantum Simulation of Reaction Dynamics by Density
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  journal =      BTjpc,
  year =         "1993",
  volume =       "97",
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@InCollection{Berendsen94,
  author =       "Herman J. C. Berendsen and David van der Spoel",
  booktitle =    "Aspects of Computational Science",
  title =        "Molecular Dynamics simulations",
  publisher =    "National Computing Facilities Foundation",
  address =      "P.O. Box 93120, 2509 AC Den Haag, The Netherlands",
  year =         "1994",
  editor =       "Aad van der Steen",
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@Article{Berendsen95a,
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@InCollection{Caflisch94,
  author =       "Amadeo Caflisch and Martin Karplus",
  booktitle =    "The Protein Folding Problem and Tertiary Structure
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  title =        "Molecular Dynamics Studies of Protein and Peptide
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  publisher =    "Birkh{\"a}user",
  year =         "1994",
  editor =       "Kenneth M. {Merz Jr.} and Scott M. {Le Grand}",
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@Article{Berendsen95b,
  author =       "H. J. C. Berendsen and J. Mavri",
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@Manual{Buuren94a,
  author =       "Aldert R. van Buuren and Herman J. C. Berendsen",
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  address =      "BIOMOS bv. Nij\-enborgh 4, 9747 AG Groningen, the
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@Proceedings{Buuren94b,
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  year =         "1994",
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@Article{Buuren94c,
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@Article{Buuren95b,
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@Article{Eastwood2010,
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% J. Chem. Theory Comput., Articles ASAP (As Soon As Publishable)
% Publication Date (Web): May 24, 2010 (Article)
% DOI: 10.1021/ct9002916


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@Manual{Marrink93b,
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@InCollection{Mavri92a,
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  year =         "1992",
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  year =         "1992",
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@Article{Mavri93a,
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  year =         "1993",
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@Article{Mavri93b,
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  year =         "1993",
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@Article{Mavri94a,
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@Article{Mavri94b,
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  author =       {B. S. ZhoBerendsen {\etal} also derived
values for 


Since $\dEdq \approx$ 

therefore $\xi$ should be about three orders of magnitude
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$\frac{\partial P}{\partial C_{12}} > 0,
\frac{\partial E}{\partial C_6}    < 0$ and
$\frac{\partial E}{\partial q}     < 0$.
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@Article{Svensson96a,
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@Article{Mu2005a,
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@Article{Shaw2005a,
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@Article{Shaw2005,
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@Article{Shaw2006,
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@Article{Shaw2007a,
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@Article{Shaw2007b,
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@Article{Bush2006a,
   author  = {I. J. Bush and I. T. Todorov and W. Smith},
  title   = {A DAFT DL_POLY1 distributed memory adaptation of the smoothed particle mesh Ewald method},
  journal = {Comput. Phys. Commun.},
  volume  = {175},
  year    = {2006},
  pages   = {323-329},
  OPTabstract = {The Smoothed Particle Mesh Ewald method [U. Essmann, L. Perera, M.L.
Berkowtz, T. Darden, H. Lee, L.G. Pedersen, J. Chem. Phys. 103 (1995)
8577] for calculating long ranged forces in molecular simulation has
been adapted for the parallel molecular dynamics code DL_POLY_3 [I.T.
Todorov, W. Smith, Philos. Trans. Roy. Soc. London 362 (2004) 18351,
making use of a novel 3D Fast Fourier Transform (DAFT) [ I.J. Bush, The
Daresbury Advanced Fourier transform, Daresbury Laboratory, 19991 that
perfectly matches the Domain Decomposition (DD) parallelisation
strategy [W. Smith, Comput. Phys. Comm. 62 (1991) 229; M.R.S. Pinches,
D. Tildesley, W. Smith, Mol. Sim. 6 (1991) 51; D. Rapaport, Comput.
Phys. Comm. 62 (1991) 217] of the DL_POLY_3 code. In this article we
describe software adaptations undertaken to import this functionality
and provide a review of its performance. (C) 2006 Elsevier B.V. All
rights reserved.
0010-4655}
}

@Article{Masella2006a,
   author  = {M. Masella},
  title   = {The multiple time step r-RESPA procedure and polarizable potentials based on induced dipole moments},
  journal = {Mol. Phys.},
  volume  = {104},
  year    = {2006},
  pages   = {415-428},
  OPTabstract = {In the present study, we present an accelerating scheme based on the
reversible multiple time step r-RESPA method to be used in molecular
dynamics simulations with polarizable potentials based on induced
dipole moments. Even if the induced dipoles are estimated with an
iterative self-consistent procedure, this scheme significantly reduces
the CPU time needed to perform a molecular dynamics simulation, up to a
factor 2, as compared to the Car-Parrinello method where additional
dynamical variables are introduced for the treatment of the induced
dipoles. The tests show that stable and reliable molecular dynamics
trajectories can be generated with that scheme, and that the physical
properties derived from the trajectories are equivalent to those
computed with the classical all atom iterative approach and the
Car-Parrinello one.
0026-8976}
}

@Article{Wang2005a,
   author  = {W. Wang and R. D. Skeel},
  title   = {Fast evaluation of polarizable forces},
  journal = {J. Chem. Phys.},
  volume  = {123},
  year    = {2005},
  pages   = {164107},
  OPTabstract = {Polarizability is considered to be the single most significant
development in the next generation of force fields for biomolecular
simulations. However, the self-consistent computation of induced atomic
dipoles in a polarizable force field is expensive due to the cost of
solving a large dense linear system at each step of a simulation. This
article introduces methods that reduce the cost of computing the
electrostatic energy and force of a polarizable model from about 7.5
times the cost of computing those of a nonpolarizable model to less
than twice the cost. This is probably sufficient for the routine use of
polarizable forces in biomolecular simulations. The reduction in
computing time is achieved by an efficient implementation of the
particle-mesh Ewald method, an accurate and robust predictor based on
least-squares fitting, and non-stationary iterative methods whose fast
convergence is accelerated by a simple preconditioner. Furthermore,
with these methods, the self-consistent approach with a larger timestep
is shown to be faster than the extended Lagrangian approach. The use of
dipole moments from previous timesteps to calculate an accurate initial
guess for iterative methods leads to an energy drift, which can be made
acceptably small. The use of a zero initial guess does not lead to
perceptible energy drift if a reasonably strict convergence criterion
for the iteration is imposed. (c) 2005 American Institute of Physics.
0021-9606}
}

@Article{Izaguirre2005a,
   author  = {J. A. Izaguirre and S. S. Hampton and T. Matthey},
  title   = {Parallel multigrid summation for the N-body problem},
  journal = {J. Parallel Distrib. Comput.},
  volume  = {65},
  year    = {2005},
  pages   = {949-962},
  OPTabstract = {An Theta(n) parallel multigrid summation method (MG) for the N-body
problem is presented. The method was originally devised for vacuum
boundary conditions. Here, it is extended to periodic boundary
conditions and implemented in parallel using force decomposition and
MPI. MG is based on a hierarchical decomposition of computational
kernels on multiple grids. For low accuracy calculations, appropriate
for molecular dynamics, a sequential implementation is as fast or
faster than particle mesh Ewald (PME). Our parallel implementation is
more scalable than PME. The method can be combined with multiple time
stepping integrators to produce a powerful simulation protocol for
simulation of biological molecules and other materials. The parallel
implementation is tested on both a Linux cluster with Myrinet
interconnect and a shared memory computer. It is available as
open-source at http://protomol.sourceforge.net. An auxiliary tool
allows the automatic selection of optimal parameters for MG, and is
available at http://mdsimaid.cse.nd.edu. (c) 2005 Elsevier Inc. All
rights reserved.
0743-7315}
}

@Article{Crocker2005a,
   author  = {M. S. Crocker and S. S. Hampton and T. Matthey and J. A. Izaguirre},
  title   = {MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms},
  journal = {J. Comput. Chem.},
  volume  = {26},
  year    = {2005},
  pages   = {1021-1031},
  OPTabstract = {MDSIMAID is a recommender system that optimizes parallel Particle Mesh
Ewald (PME) and both sequential and parallel multigrid (MG) summation
fast electrostatic solvers. MDSIMAID optimizes the running time or
parallel scalability of these methods within a given error tolerance.
MDSIMAID performs a run time constrained search on the parameter space
of each method starting from semiempirical performance models.
Recommended parameters are presented to the user. MDSIMAID'S
optimization of MG leads to configurations that are up to 14 times
faster or 17 times more accurate than published recommendations.
Optimization of PME can improve its parallel scalability, making it run
twice as fast in parallel in our tests. MDSIMAID and its Python source
code are accessible through a Web portal located at
http://mdsimaid.cse.nd.edu. (c) 2005 Wiley Periodicals, Inc.
0192-8651}
}

@Article{Germain2005a,
   author  = {R. S. Germain and Y. Zhestkov and M. Eleftheriou and A. Rayshubskiy and F. Suits and T. J. C. Ward and B. G. Fitch},
  title   = {Early performance data on the Blue Matter molecular simulation framework},
  journal = {IBM J. Res. Dev.},
  volume  = {49},
  year    = {2005},
  pages   = {447-455},
  OPTabstract = {Blue Matter is the application framework being developed in conjunction
with the scientific portion of the IBM Blue Gene(&REG;) project. We
describe the parallel decomposition currently, being used to target the
Blue Gene/L machine and discuss the application-based trace tools used
to analyze the performance of the application. We also present the
resuits of early performace studies, including a comparison of the
performance of the Ewald and the particle-particle particle-mesh (P3ME)
methods, compare the measured performance of some key collective
operations with the limitations imposed by the hardware, and discuss
some future directions for research.
0018-8646}
}

@Article{Peter2002a,
   author  = {C. Peter and W. F. van Gunsteren and P. H. Hunenberger},
  title   = {Solving the Poisson equation for solute-solvent systems using fast Fourier transforms},
  journal = {J. Chem. Phys.},
  volume  = {116},
  year    = {2002},
  pages   = {7434-7451},
  OPTabstract = {An iterative algorithm based on fast Fourier transforms is proposed to
solve the Poisson equation for systems of heterogeneous permittivity
(e.g., solute cavity in a solvent) under periodic boundary conditions.
The method makes explicit use of the dipole-dipole interaction tensor,
and is thus easily generalizable to arbitrary forms of electrostatic
interactions (e.g., Coulomb's law with straight or smooth cutoff
truncation). The convergence properties of the algorithm and the
influence of various model parameters are investigated in detail, and a
set of appropriate values for these parameters is determined. The
algorithm is further tested by application to three types of systems (a
single spherical ion, two spherical ions, and small biomolecules), and
comparison with analytical results (single ion) and with results
obtained using a finite-difference solver under periodic boundary
conditions. The proposed algorithm performs very well in terms of
accuracy and convergence properties, with an overall speed comparable
in the current implementation to that of a typical finite-difference
solver. Future developments and applications of the algorithm will
include: (i) the assessment of periodicity- and cutoff-induced
artifacts in explicit-solvent simulations; (ii) the design of new
electrostatic schemes for explicit-solvent simulations mimicking more
accurately bulk solution; (iii) a faster evaluation of solvation free
energies based on continuum electrostatics in cases where
periodicity-induced artifacts can be neglected. (C) 2002 American
Institute of Physics.
0021-9606}
}

@Article{Beckers1998a,
   author  = {J. V. L. Beckers and C. P. Lowe and S. W. De Leeuw},
  title   = {An iterative PPPM method for simulating Coulombic systems on distributed memory parallel computers},
  journal = {Mol. Simul.},
  volume  = {20},
  year    = {1998},
  pages   = {369-383},
  OPTabstract = {We describe results obtained from a new implementation of Hockney's
Particle-Particle Particle-Mesh (PPPM) method for evaluation of Coulomb
energies and forces in simulations of charged particles. Rather than
taking the usual approach, solving Poisson's equation by means of a
Fourier transformation, we use an iterative Poisson solver. In a
molecular dynamics (MD) simulation the solution from the previous
time-step provides a good starting point for the next solution. This
reduces the number of iterations per time-step to acceptable values.
The iterative scheme has a complexity O(N), and, in contrast with the
Fourier transform based approach, it is easily implemented on a
parallel architecture with a minimum of communication overhead.
We examine the origin of the errors in the algorithm and find that
reasonable accuracies in the Coulomb interaction can best be attained
by making the charge density profile as smooth as possible. This
involves spreading the particle charges over a large number of grid
points. Assigning these charges then becomes the most time consuming
part of the algorithm. We show how we can then gain a considerable
saving in computing time by employing a diffusion equation as a charge
spreading mechanism.
The effect of employing the algorithm with an accuracy less than that
typically tolerated in an Ewald summation is studied by computing, from
an MD simulation of silica, quantities that are sensitive to the long
range part of the Coulomb interaction. These results are compared to
full Ewald sum reference simulations and found to be within the
statistical error.
0892-7022}
}

@Article{Meloni2007,
  author =       {Simone Meloni and Mario Rosati},
  title =        {Efficient partilce labeling in atomistic simulations},
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  year =         {2007},
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}

@InProceedings{Clark91,
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                            F. Suits and W. Swope and T.J.C. Ward  and Y. Zhestkov
                             and R. Zhou",
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  volume = "63",
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  pages =        "759--773",
}

@Article{Nelson96,
  author =       "M.T. Nelson and W. Humphrey and A. Gursoy and A.  Dalke
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  year =         {1996},
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}

@Article{Jorgensen1996,
  author =       {W. L. Jorgensen and D. S. Maxwell and J. Tirado-Rives},
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        year = {2007},
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@article{Rhee2004a,
        author = {Young Min Rhee and Eric J. Sorin and Guha Jayachandran and Erik Lindahl
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        year = {2004},
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@Article{Hess2008a,
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@Article{Harmandaris2007,
  author =       {Vagelis A. Harmandaris and Dirk Reith and Nico F. A. van der Vegt and Kurt Kremer},
  title =        {Comparison Between Coarse-Graining Models for Polymer Systems: Two Mapiing Schemes for Polystyrene},
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  year =         2007,
  volume =       {208},
  pages =        {2109--2120}
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@Article{Liem1991,
  author =       {S. Y. Liem and D. Brown and J. H. R. Clarke},
  title =        {Molecular dynamics simulations on distributed memory machines},
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  author =       {Brad Lee Holian and Arthur F. Voter and Ramon Ravelo},
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@Article{Phillips2005,
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@Article{Limbach06a,
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@Article{Kutzner2011,
  author    = {C. Kutzner and J. Czub and H. Grubm{\"u}ller},
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        title = {Versatile {Object-Oriented} Toolkit for {Coarse-Graining} Applications},
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@article{wang_jpcb10,
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  title = {A biomolecular force field based on the free enthalpy of hydration and solvation: The {GROMOS} force-field parameter sets {53A5} and {53A6}},
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@article{Pronk2013,
  author = {Pronk, Sander and P{\'a}ll, Szil{\'a}rd and Schulz, Roland and Larsson, Per and Bjelkmar, P{\"a}r 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},
  volume = {29},
  number = {7},
  pages = {845-854},
  year = {2013},
  doi = {10.1093/bioinformatics/btt055},
  abstract ={Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources.Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.Availability: GROMACS is an open source and free software available from http://www.gromacs.org.Contact: erik.lindahl@scilifelab.seSupplementary information: Supplementary data are available at Bioinformatics online.},
  URL = {http://bioinformatics.oxfordjournals.org/content/29/7/845.abstract},
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  journal = {Bioinformatics}
}

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year = {2000},
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@incollection {Pall2015,
author = {P{\'a}ll, Szil{\'a}rd and Abraham, Mark James and Kutzner, Carsten and Hess, Berk and Lindahl, Erik},
title = { Tackling Exascale Software Challenges in Molecular Dynamics Simulati\
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