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  • 1
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 116 (1994), S. 7451-7452 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 100 (1978), S. 3255-3256 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 92 (1990), S. 1359-1361 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The contribution of the solvent molecules to the potentials of mean force between two water molecules in selected fixed relative orientations was calculated as a function of the interoxygen distance using the probability ratio method with adaptive umbrella sampling in Monte Carlo computer simulations.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 2118-2129 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Results are presented from potential energy minimization of water clusters and from molecular dynamics and Monte Carlo simulations of a liquid water droplet model. A new method for molecular dynamics—the implicit-Euler/Langevin scheme—is used in combination with a truncated Newton minimizer for potential energy functions. Structural and thermodynamic properties are reported for the scheme (with time steps of 5 and 10 fs), compared to a standard explicit formulation (with Δt=1 fs), to a Monte Carlo simulation, and to available experimental data. Results demonstrate that the implicit scheme is computationally feasible for large-scale biomolecular simulations, and that the droplet model can reasonably reproduce general structural features of liquid water. Results also show that the desired behavior is obtained from the implicit formulation: stability over large time steps, and effective damping of the high-frequency vibrational modes. Thus, major "bulk'' properties of the system of interest may be observed more rapidly.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 1059-1060 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The cavity-biased grand canonical ensemble Monte Carlo simulation method has been compared with a particular implementation of the grand canonical ensemble molecular dynamics method by examining the fluctuations during simulations of equivalent length. The Monte Carlo run exhibited an order of magnitude faster fluctuation than the molecular dynamics run. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 419-426 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The potentials of mean force between sodium and chloride ions and between sodium and dimethylphosphate ions in aqueous solution are calculated by the probability ratio method using adaptive umbrella sampling Monte Carlo with a variety of simulation setups. The potential of mean force of sodium chloride is found to have only one minimum in contradiction to earlier molecular dynamics results with the same intermolecular potentials, but different boundary conditions. Our result in the region of contradiction is supported by large system size and free energy perturbation calculations. It is established that the difference is due to the respective boundary condition schemes employed. This result is to be regarded as a consequence of the potential function scheme employed and not necessarily as a statement about actual aqueous sodium chloride. A similar dependence of the existence of the second minimum on boundary conditions is observed for the sodium-dimethylphosphate PMF. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 6126-6140 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Using the concepts of scaled particle theory, an analytical theory is developed to investigate the limiting behavior of solvation free energies at the particle creation limit. The new theory directly incorporates the weakly attractive, dispersion interaction terms into the analytical calculations. For neutral molecular systems, the effects of longer ranged electrostatic interactions are also incorporated, albeit in an ad hoc way, and the validity of the utilized assumptions are then demonstrated with numerical examples. It is shown that it is possible to blend the numerical and analytical methods to increase the reliability of quantitative results, and, at the same time, to achieve savings on computational expenditure for certain types of calculations. Different methods of performing the thermodynamic integration in solvation free energy calculations are also compared. Studied examples clearly show the importance of proper treatment of the divergence at the particle creation limit in obtaining quantitatively reliable results for the solvation free energies.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 10770-10773 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The cavity-biased grand-canonical ensemble method was applied to the simulation of a lipid bilayer using an enhanced Monte Carlo sampling technique. The enhancements include controlling the torsion and molecular rotation step size based on the lipid's conformation and controlling the order of torsion change attempts. It was found that the proposed sampling technique significantly enhances the rate of sampling of the lipid conformations while the grand-canonical ensemble implementation ensures that the water can both penetrate and escape pockets in the bilayer. The latter will be particularly important for simulating bilayers with embedded molecules. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 2991-3002 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new effective pair potential model is proposed for computer simulations of liquid methylene fluoride and used in Monte Carlo simulations on the isothermal-isobaric ensemble at two different temperatures. The new model is able to reproduce the thermodynamic (internal energy, density, heat capacity, vapor-liquid equilibrium) and structural (neutron diffraction data) properties of liquid methylene fluoride with good accuracy. The structure of liquid methylene fluoride is analyzed in detail on the basis of the present simulation at 153 K. It is found that, unlike in liquid water, the preferential location of the nearest neighbors is in the direction of the face centers of the tetrahedron of the central molecule. However, the four nearest neighbors do not surround the central molecule in a highly tetrahedral arrangement: the obtained distribution of the tetrahedral angular order parameter is rather similar to that in liquid argon. Preferential head-to-tail type orientation is found for nearest neighbors, accompanied by a slight preference for antiparallel dipole–dipole arrangement. The orientational correlation of the molecules is found to be rather long ranged, extending over the first coordination shell. The observed preferential nearest neighbor arrangement is resulted from the competition of steric and electrostatic interactions. No evidence for C–H⋅⋅⋅⋅F type hydrogen bonding is found in liquid methylene fluoride. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 88 (1984), S. 3180-3182 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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