Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters

We compared molecular dynamics simulations of a bilayer of 128 fully hydrated phospholipid (DPPC) molecules, using different parameters and macroscopic boundary conditions. The same system was studied under constant pressure, constant volume, and constant surface tension boundary conditions, with two different sets of charges, the single point charge (SPC) and extended single point charge (SPC/E) water model and two different sets of Lennard‐Jones parameters for the interaction between water and methyl/methylene. Some selected properties of the resulting bilayer systems are compared to each other, previous simulations, and experimental data. It is concluded that in relatively high water concentration it is possible to use ab initio derived charges with constant pressure boundary conditions. The SPC water model gives a larger area per head group and a broader interface than the SPC/E model. Increasing the repulsion between water oxygens and CH2/CH3 groups has a large effect on the width of the interface an...

[1]  P. Weiner,et al.  Computer Simulation of Biomolecular Systems , 1997 .

[2]  H. Berendsen,et al.  Molecular dynamics simulation of a charged biological membrane , 1996 .

[3]  Bernard R. Brooks,et al.  Computer simulation of liquid/liquid interfaces. I. Theory and application to octane/water , 1995 .

[4]  R. Pastor,et al.  Computer simulation of liquid/liquid interfaces. II. Surface tension-area dependence of a bilayer and monolayer , 1995 .

[5]  E. Jakobsson,et al.  Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. , 1995, Biophysical journal.

[6]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[7]  Wilfred F. van Gunsteren,et al.  Lattice‐sum methods for calculating electrostatic interactions in molecular simulations , 1995 .

[8]  W. Richards,et al.  Head group and chain behavior in biological membranes: a molecular dynamics computer simulation. , 1994, Biophysical journal.

[9]  Herman J. C. Berendsen,et al.  Simulation of Water Transport through a Lipid Membrane , 1994 .

[10]  P. Huang,et al.  Molecular dynamics simulations of phospholipid bilayers. , 1994, Journal of biomolecular structure & dynamics.

[11]  K V Damodaran,et al.  A comparison of DMPC- and DLPE-based lipid bilayers. , 1994, Biophysical journal.

[12]  Herman J. C. Berendsen,et al.  Molecular dynamics simulation of a membrane/water interface: the ordering of water and its relation to the hydration force , 1993 .

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

[14]  Herman J. C. Berendsen,et al.  A Molecular Dynamics Study of the Decane/Water Interface , 1993 .

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

[16]  Terry R. Stouch,et al.  Computer simulation of a phospholipid monolayer‐water system: The influence of long range forces on water structure and dynamics , 1993 .

[17]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[18]  B. Guillot,et al.  A computer simulation study of the liquid–vapor coexistence curve of water , 1993 .

[19]  J. Nagle,et al.  Area/lipid of bilayers from NMR. , 1993, Biophysical journal.

[20]  V A Parsegian,et al.  Membrane dipole potentials, hydration forces, and the ordering of water at membrane surfaces. , 1992, Biophysical journal.

[21]  S H White,et al.  Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure. , 1992, Biophysical journal.

[22]  B. Pullman,et al.  Membrane Proteins: Structures, Interactions and Models , 1992 .

[23]  R. Thurmond,et al.  Molecular areas of phospholipids as determined by 2H NMR spectroscopy. Comparison of phosphatidylethanolamines and phosphatidylcholines. , 1991, Biophysical journal.

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

[25]  T. McIntosh,et al.  Magnitude of the solvation pressure depends on dipole potential. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Wilfred F. van Gunsteren,et al.  Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , 1989 .

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

[28]  J. Hermans,et al.  Excess free energy of liquids from molecular dynamics simulations. Application to water models. , 1988, Journal of the American Chemical Society.

[29]  K. Dill,et al.  Solute partitioning into lipid bilayer membranes. , 1988, Biochemistry.

[30]  J. Nagle,et al.  Structure of fully hydrated bilayer dispersions. , 1988, Biochimica et biophysica acta.

[31]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

[32]  T. McIntosh,et al.  Hydration force and bilayer deformation: a reevaluation. , 1986, Biochemistry.

[33]  D. Griffiths,et al.  X-ray structure study of thermotropic phases in isoacylphosphatidylcholine multibilayers. , 1986, Biophysical journal.

[34]  W. Hubbell,et al.  The membrane dipole potential in a total membrane potential model. Applications to hydrophobic ion interactions with membranes. , 1986, Biophysical journal.

[35]  F. Jähnig.  Lipid exchange between membranes. , 1984, Biophysical journal.

[36]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[37]  D. Engelman,et al.  Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles. , 1983, Journal of molecular biology.

[38]  G. Shipley,et al.  Characterization of the sub-transition of hydrated dipalmitoylphosphatidylcholine bilayers. Kinetic, hydration and structural study , 1982 .

[39]  R. Pace,et al.  Molecular motions in lipid bilayers. I. Statistical mechanical model of acyl chain motion , 1982 .

[40]  Herman J. C. Berendsen,et al.  MOLECULAR-DYNAMICS SIMULATION OF A BILAYER-MEMBRANE , 1982 .

[41]  L. J. Lis,et al.  Interactions between neutral phospholipid bilayer membranes. , 1982, Biophysical journal.

[42]  W. L. Jorgensen.  Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water , 2002 .

[43]  John F. Nagle,et al.  Theory of the Main Lipid Bilayer Phase Transition , 1980 .

[44]  J. Seelig,et al.  Lipid conformation in model membranes and biological membranes , 1980, Quarterly Reviews of Biophysics.

[45]  T. Mitsui,et al.  Structural Parameters of Dipalmitoyl Phosphatidylcholine Lamellar Phases and Bilayer Phase Transitions , 1978 .

[46]  J. Seelig.  Deuterium magnetic resonance: theory and application to lipid membranes , 1977, Quarterly Reviews of Biophysics.

[47]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[48]  G. Shipley,et al.  Nature of the Thermal pretransition of synthetic phospholipids: dimyristolyl- and dipalmitoyllecithin. , 1976, Biochemistry.

[49]  J. Seelig,et al.  Deuterium order parameters in relation to thermodynamic properties of a phospholiped bilayer. A statistical mechanical interpretation. , 1975, Biochemistry.

[50]  G. S. Rushbrooke.  Introduction to statistical mechanics , 1949 .