Molecular dynamics simulation of the dipalmitoylphosphatidylcholine (DPPC) lipid bilayer in the fluid phase using the Nosé-Parrinello-Rahman NPT ensemble

Abstract A dipalmitoylphosphatidylcholine (DPPC) bilayer could successfully be simulated in the Nose-Parrinello-Rahman NPT ensemble from an arbitrarily generated crystal-like initial configuration. The initial condition dependence may be small and various artefacts, which were found in molecular dynamics calculations with rectangular cells, could be avoided.

[1]  K. Schulten,et al.  Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase , 1993 .

[2]  H. Hauser,et al.  Preferred conformation and molecular packing of phosphatidylethanolamine and phosphatidylcholine. , 1981, Biochimica et biophysica acta.

[3]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[4]  K V Damodaran,et al.  Structure and dynamics of the dilauroylphosphatidylethanolamine lipid bilayer. , 1992, Biochemistry.

[5]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[6]  R M Venable,et al.  Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity. , 1993, Science.

[7]  Terry R. Stouch,et al.  Lipid Membrane Structure and Dynamics Studied by All-Atom Molecular Dynamics Simulations of Hydrated Phospholipid Bilayers , 1993 .

[8]  V. Parsegian,et al.  Hydration forces between phospholipid bilayers , 1989 .

[9]  S. Nosé,et al.  Constant pressure molecular dynamics for molecular systems , 1983 .

[10]  S. Nosé.  A unified formulation of the constant temperature molecular dynamics methods , 1984 .

[11]  H. Berendsen,et al.  Molecular dynamics simulation of a smectic liquid crystal with atomic detail , 1988 .

[12]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[13]  H. C. Andersen.  Molecular dynamics simulations at constant pressure and/or temperature , 1980 .

[14]  J. Tabony,et al.  Quasielastic neutron scattering measurements of fast local translational diffusion of lipid molecules in phospholipid bilayers. , 1991, Biochimica et biophysica acta.

[15]  S. Okazaki,et al.  Molecular dynamics study of the lauryl alcohol-laurate model bilayer. , 1993, Biophysical journal.

[16]  J. Seelig,et al.  The dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance. , 1974, Biochemistry.

[17]  Barry J. Hardy,et al.  Conformational sampling of hydrocarbon and lipid chains in an orienting potential , 1994, J. Comput. Chem..

[18]  R. Pearson,et al.  The molecular structure of lecithin dihydrate , 1979, Nature.