Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.
暂无分享,去创建一个
Wilfred F van Gunsteren | Siewert J Marrink | Riccardo Baron | Daniel Trzesniak | Andreas Elsener | Alex H de Vries | R. Baron | W. V. van Gunsteren | A. Elsener | S. Marrink | D. Trzesniak | A. D. de Vries | A. H. de Vries
[1] Wilfred F. van Gunsteren,et al. A novel approach for designing simple point charge models for liquid water with three interaction sites , 2003, J. Comput. Chem..
[2] Charles L. Brooks,et al. Thermodynamics of aqueous solvation: Solution properties of alcohols and alkanes , 1987 .
[3] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[4] Chris Oostenbrink,et al. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..
[5] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[6] Marcus Müller,et al. Coarse‐grained models and collective phenomena in membranes: Computer simulation of membrane fusion , 2003 .
[7] William L. Jorgensen,et al. Relative partition coefficients for organic solutes from fluid simulations , 1990 .
[8] Christophe Chipot,et al. Free Energy Calculations. The Long and Winding Gilded Road , 2002 .
[9] Wilfred F van Gunsteren,et al. Biomolecular modeling: Goals, problems, perspectives. , 2006, Angewandte Chemie.
[10] Y. Guissani,et al. A computer simulation study of the temperature dependence of the hydrophobic hydration , 1993 .
[11] W. F. V. Gunsteren,et al. Biomolekulare Modellierung: Ziele, Probleme, Perspektiven , 2006 .
[12] N. Bodor,et al. A new method for the estimation of partition coefficient , 1989 .
[13] Wilfred F. van Gunsteren,et al. An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase , 2001, J. Comput. Chem..
[14] Valentina Tozzini,et al. Coarse-grained models for proteins. , 2005, Current opinion in structural biology.
[15] Reinhard Lipowsky,et al. Computer simulations of bilayer membranes - self-assembly and interfacial tension. , 1998 .
[16] G. Graziano. Entropy convergence in the hydration thermodynamics of n-alcohols. , 2005, The journal of physical chemistry. B.
[17] K. Esselink,et al. Computer simulations of a water/oil interface in the presence of micelles , 1990, Nature.
[18] X. Daura,et al. Parametrization of aliphatic CHn united atoms of GROMOS96 force field , 1998 .
[19] Mark A. Miller,et al. Why is it so difficult to simulate entropies, free energies, and their differences? , 2001, Accounts of chemical research.
[20] A. Mark,et al. Molecular view of hexagonal phase formation in phospholipid membranes. , 2004, Biophysical journal.
[21] J. Hermans,et al. Excess free energy of liquids from molecular dynamics simulations. Application to water models. , 1988, Journal of the American Chemical Society.
[22] Alessandra Villa,et al. Calculation of the free energy of solvation for neutral analogs of amino acid side chains , 2002, J. Comput. Chem..
[23] Berk Hess,et al. GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .
[24] Arieh Ben-Naim,et al. Solvation thermodynamics of nonionic solutes , 1984 .
[25] Development of QSAR's based on high performance liquid chromatography capacity factors to describe non-specific toxicity , 1989 .
[26] Reinhard Lipowsky,et al. The computational route from bilayer membranes to vesicle fusion , 2006, Journal of physics. Condensed matter : an Institute of Physics journal.
[27] Klaus Schulten,et al. Coarse grained protein-lipid model with application to lipoprotein particles. , 2006, The journal of physical chemistry. B.
[28] T. P. Straatsma,et al. Free Energy by Molecular Simulation , 2007 .
[29] Florian Müller-Plathe,et al. Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back. , 2002, Chemphyschem : a European journal of chemical physics and physical chemistry.
[30] Wilfred F van Gunsteren,et al. Energy-entropy compensation in the transfer of nonpolar solutes from water to cosolvent/water mixtures. , 2004, Chemphyschem : a European journal of chemical physics and physical chemistry.
[31] Y. Guissani,et al. A computer‐simulation study of hydrophobic hydration of rare gases and of methane. I. Thermodynamic and structural properties , 1991 .
[32] W. F. van Gunsteren,et al. Entropic Contributions in Cosolvent Binding to Hydrophobic Solutes in Water , 2004 .
[33] D. Tildesley,et al. On the role of hydrodynamic interactions in block copolymer microphase separation , 1999 .
[34] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[35] Roland Faller,et al. Simulation of domain formation in DLPC-DSPC mixed bilayers. , 2004, Langmuir : the ACS journal of surfaces and colloids.
[36] Kazimierz Krynicki,et al. Pressure and temperature dependence of self-diffusion in water , 1978 .
[37] Wilfred F. van Gunsteren,et al. Computer simulation studies on the solvation of aliphatic hydrocarbons in 6.9 M aqueous urea solution , 2004 .
[38] B. Widom,et al. Some Topics in the Theory of Fluids , 1963 .
[39] W. V. van Gunsteren,et al. Estimating entropies from molecular dynamics simulations. , 2004, The Journal of chemical physics.
[40] Kurt Kremer,et al. Computer simulations for macromolecular science , 2003 .
[41] Martin Karplus,et al. A thermodynamic analysis of solvation , 1988 .
[42] Wilfred F van Gunsteren,et al. Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates. , 2006, The journal of physical chemistry. B.
[43] A. Mark,et al. Coarse grained model for semiquantitative lipid simulations , 2004 .
[44] H. Berendsen,et al. Interaction Models for Water in Relation to Protein Hydration , 1981 .
[45] P. Schatzberg. SOLUBILITIES OF WATER IN SEVERAL NORMAL ALKANES FROM C7 TO C161 , 1963 .
[46] D. J. Tildesley,et al. Computer simulation of molecular liquid mixtures. I. A diatomic Lennard‐Jones model mixture for CO2/C2H6 , 1986 .
[47] Kurt Kremer,et al. Bridging the Gap Between Atomistic and Coarse-Grained Models of Polymers: Status and Perspectives , 2000 .
[48] R. C. Reeder,et al. A Coarse Grain Model for Phospholipid Simulations , 2001 .
[49] Siewert J Marrink,et al. Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. , 2005, Chemistry and physics of lipids.
[50] A. Mark,et al. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations , 1994 .
[51] Sergei Izvekov,et al. Multiscale Coarse-Graining of Mixed Phospholipid/Cholesterol Bilayers. , 2006, Journal of chemical theory and computation.
[52] Markus Christen,et al. The GROMOS software for biomolecular simulation: GROMOS05 , 2005, J. Comput. Chem..
[53] Peter J Bond,et al. Insertion and assembly of membrane proteins via simulation. , 2006, Journal of the American Chemical Society.
[54] D. C. Douglass,et al. Diffusion in Paraffin Hydrocarbons , 1958 .
[55] R. Baron,et al. Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations. , 2006, The journal of physical chemistry. B.
[56] P. Weiner,et al. Computer Simulation of Biomolecular Systems , 1997 .
[57] Peter A. Kollman,et al. FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .
[58] Wilfred F. van Gunsteren,et al. Computation of free energy , 2002 .
[59] Wilfred F. van Gunsteren,et al. A molecular dynamics simulation study of chloroform , 1994 .
[60] D. Beveridge,et al. Free energy via molecular simulation: applications to chemical and biomolecular systems. , 1989, Annual review of biophysics and biophysical chemistry.
[61] Jonathan W. Essex,et al. Relative partition coefficients from partition functions: a theoretical approach to drug transport , 1989 .
[62] R. C. Weast. CRC Handbook of Chemistry and Physics , 1973 .
[63] Gerald J. Niemi,et al. Prediction of octanol/water partition coefficient ( K OW ) with algorithmically derived variables , 1992 .