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11. Klein ML, Shinoda W (2008) Large-scale molecular dynamics simulations of self-assembling
systems. Science 321(5890):798–800
12. Andersen HC (1980) Molecular-dynamics simulations at constant pressure and-or temperature.
J Chem Phys 72(4):2384–2393
13. Nose ´ S, Klein ML (1983) Constant pressure molecular dynamics for molecular systems.
Mol Phys 50(5):1055–1076
14. Nose ´ S (1984) A unified formulation of the constant temperature molecular-dynamics
methods. J Chem Phys 81(1):511–519
15. Jorgensen WL et al (1983) Comparison of simple potential functions for simulating liquid
water. J Chem Phys 79:926–935
16. MacKerell AD et al (1998) All-atom empirical potential for molecular modeling and dynamics
studies of proteins. J Phys Chem B 102(18):3586–3616
17. Cornell WD et al (1995) A 2nd generation force-field for the simulation of proteins, nucleicacids, and organic-molecules. J Am Chem Soc 117(19):5179–5197
18. Jorgensen WL, Maxwell DS, TiradoRives J (1996) Development and testing of the OPLS
all-atom force field on conformational energetics and properties of organic liquids. J Am Chem
Soc 118(45):11225–11236
19. Klauda JB et al (2010) Update of the CHARMM all-atom additive force field for lipids:
validation on six lipid types. J Phys Chem B 114(23):7830–7843
20. Kirkwood JG (1935) Statistical mechanics of fluid mixtures. J Chem Phys 3(5):300–313
21. Torrie GM, Valleau JP (1977) Monte-Carlo study of a phase-separating liquid-mixture by
umbrella sampling. J Chem Phys 66(4):1402–1408
22. Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein
folding. Chem Phys Lett 314(1–2):141–151
23. Swendsen RH, Wang JS (1986) Replica Monte-Carlo simulation of spin-glasses. Phys Rev
Lett 57(21):2607–2609
24. Shelley JC et al (2001) A coarse grain model for phospholipid simulations. J Phys Chem B 105
(19):4464–4470
25. Shinoda W, Devane R, Klein ML (2007) Multi-property fitting and parameterization of a
coarse grained model for aqueous surfactants. Mol Simul 33(1–2):27–36
26. Smit B et al (1990) Computer-simulations of a water oil interface in the presence of micelles.
Nature 348(6302):624–625
27. Marrink SJ et al (2007) The MARTINI force field: coarse grained model for biomolecular
simulations. J Phys Chem B 111(27):7812–7824
28. Brannigan G, Brown FLH (2004) Solvent-free simulations of fluid membrane bilayers. J Chem
Phys 120(2):1059–1071
29. Cooke IR, Kremer K, Deserno M (2005) Tunable generic model for fluid bilayer membranes.
Phys Rev E 72(1):011506
30. Goetz R, Lipowsky R (1998) Computer simulations of bilayer membranes: self-assembly and
interfacial tension. J Chem Phys 108(17):7397–7409
31. Lopez CF et al (2002) Self-assembly of a phospholipid Langmuir monolayer using coarsegrained molecular dynamics simulations. J Phys-Condens Matter 14(40):9431–9444
32. Ercolessi F, Adams JB (1994) Interatomic potentials from 1st-principles calculations – the
force-matching method. Europhys Lett 26(8):583–588
33. Noid WG et al (2008) The multiscale coarse-graining method. II. Numerical implementation
for coarse-grained molecular models. J Chem Phys 128(24):244115
34. Noid WG et al (2008) The multiscale coarse-graining method. I. A rigorous bridge between
atomistic and coarse-grained models. J Chem Phys 128(24):244114
106
G. Fiorin et al.
277(5330):1232–1237
10. Whitesides GM, Grzybowski B (2002) Self-assembly at all scales. Science 295(5564):
2418–2421
11. Klein ML, Shinoda W (2008) Large-scale molecular dynamics simulations of self-assembling
systems. Science 321(5890):798–800
12. Andersen HC (1980) Molecular-dynamics simulations at constant pressure and-or temperature.
J Chem Phys 72(4):2384–2393
13. Nose ´ S, Klein ML (1983) Constant pressure molecular dynamics for molecular systems.
Mol Phys 50(5):1055–1076
14. Nose ´ S (1984) A unified formulation of the constant temperature molecular-dynamics
methods. J Chem Phys 81(1):511–519
15. Jorgensen WL et al (1983) Comparison of simple potential functions for simulating liquid
water. J Chem Phys 79:926–935
16. MacKerell AD et al (1998) All-atom empirical potential for molecular modeling and dynamics
studies of proteins. J Phys Chem B 102(18):3586–3616
17. Cornell WD et al (1995) A 2nd generation force-field for the simulation of proteins, nucleicacids, and organic-molecules. J Am Chem Soc 117(19):5179–5197
18. Jorgensen WL, Maxwell DS, TiradoRives J (1996) Development and testing of the OPLS
all-atom force field on conformational energetics and properties of organic liquids. J Am Chem
Soc 118(45):11225–11236
19. Klauda JB et al (2010) Update of the CHARMM all-atom additive force field for lipids:
validation on six lipid types. J Phys Chem B 114(23):7830–7843
20. Kirkwood JG (1935) Statistical mechanics of fluid mixtures. J Chem Phys 3(5):300–313
21. Torrie GM, Valleau JP (1977) Monte-Carlo study of a phase-separating liquid-mixture by
umbrella sampling. J Chem Phys 66(4):1402–1408
22. Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein
folding. Chem Phys Lett 314(1–2):141–151
23. Swendsen RH, Wang JS (1986) Replica Monte-Carlo simulation of spin-glasses. Phys Rev
Lett 57(21):2607–2609
24. Shelley JC et al (2001) A coarse grain model for phospholipid simulations. J Phys Chem B 105
(19):4464–4470
25. Shinoda W, Devane R, Klein ML (2007) Multi-property fitting and parameterization of a
coarse grained model for aqueous surfactants. Mol Simul 33(1–2):27–36
26. Smit B et al (1990) Computer-simulations of a water oil interface in the presence of micelles.
Nature 348(6302):624–625
27. Marrink SJ et al (2007) The MARTINI force field: coarse grained model for biomolecular
simulations. J Phys Chem B 111(27):7812–7824
28. Brannigan G, Brown FLH (2004) Solvent-free simulations of fluid membrane bilayers. J Chem
Phys 120(2):1059–1071
29. Cooke IR, Kremer K, Deserno M (2005) Tunable generic model for fluid bilayer membranes.
Phys Rev E 72(1):011506
30. Goetz R, Lipowsky R (1998) Computer simulations of bilayer membranes: self-assembly and
interfacial tension. J Chem Phys 108(17):7397–7409
31. Lopez CF et al (2002) Self-assembly of a phospholipid Langmuir monolayer using coarsegrained molecular dynamics simulations. J Phys-Condens Matter 14(40):9431–9444
32. Ercolessi F, Adams JB (1994) Interatomic potentials from 1st-principles calculations – the
force-matching method. Europhys Lett 26(8):583–588
33. Noid WG et al (2008) The multiscale coarse-graining method. II. Numerical implementation
for coarse-grained molecular models. J Chem Phys 128(24):244115
34. Noid WG et al (2008) The multiscale coarse-graining method. I. A rigorous bridge between
atomistic and coarse-grained models. J Chem Phys 128(24):244114
106
G. Fiorin et al.