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  • 1
    Electronic Resource
    Electronic Resource
    Peptides in ionic solutions: A comparison of the Ewald and switching function techniques (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 8430-8441 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The methodological dependence of observed ion–peptide associations in molecular dynamics simulations is investigated. We compare the results from several simulations of a pentapeptide in explicit solvent and salt ions which differ in the their treatment of the long ranged electrostatic interactions. Results for both the Ewald and switching function techniques are presented. It was found that there were important differences between the two methods for the water dipole–dipole temporal and spatial correlations, total dipole moment fluctuations, and self-diffusion constants. Electrostatic potentials calculated in the region of the peptide are also used to illustrate the large differences that can arise from different treatments of the electrostatic interactions. It appears that the switching function distorts the molecular electrostatic potential experienced by the salt ions to such a degree that their behaviour becomes highly dependent on the initial conditions. In summary, the use of a switching function is not recommended for the simulation of ions and their interactions with biomolecules.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.461272
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  • 2
    Electronic Resource
    Electronic Resource
    Ewald artifacts in liquid state molecular dynamics simulations (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 4289-4293 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: An investigation into the effects of the anisotropic nature of the Ewald potential for the treatment of long range electrostatic interactions in liquid solutions has been performed. The rotational potential energy surface for two simple charge distributions, and a small protein, have been studied under conditions typically implemented in current biomolecular simulations. A transition between hindered and free rotation is observed which can be modeled quantitatively for simple charge distributions. For most systems in aqueous solution, the transition involves an energy change well below kBT. It is argued that, for solvents with a reasonably high relative permittivity, Ewald artifacts will be small and in many cases may be safely ignored. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.472246
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  • 3
    Electronic Resource
    Electronic Resource
    STABILITY IN DISEQUILIBRIUM MACRO MODELS (1976)
    Oxford, UK : Blackwell Publishing Ltd
    Metroeconomica 28 (1976), S. 0 
    Details
    ISSN: 1467-999X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Economics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1467-999X.1976.tb00548.x
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  • 4
    Electronic Resource
    Electronic Resource
    MARKOV PROCESSES AND INVESTMENT BEHAVIOR (1966)
    Oxford, UK : Blackwell Publishing Ltd
    Metroeconomica 18 (1966), S. 0 
    Details
    ISSN: 1467-999X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Economics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1467-999X.1966.tb00396.x
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  • 5
    Electronic Resource
    Electronic Resource
    A GAME-THEORETIC INTERPRETATION OF A LEONTIEF INPUT-OUTPUT SYSTEM (1963)
    Oxford, UK : Blackwell Publishing Ltd
    Metroeconomica 15 (1963), S. 0 
    Details
    ISSN: 1467-999X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Economics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1467-999X.1963.tb00520.x
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  • 6
    Electronic Resource
    Electronic Resource
    Quenched molecular dynamics simulations of tuftsin and proposed cyclic analogs (1992)
    s.l. : American Chemical Society
    Journal of medicinal chemistry 35 (1992), S. 2870-2881 
    Details
    ISSN: 1520-4804
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/jm00093a021
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  • 7
    Electronic Resource
    Electronic Resource
    Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations (1993)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 97 (1993), S. 2009-2014 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100111a046
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  • 8
    Electronic Resource
    Electronic Resource
    A generalized reaction field method for molecular dynamics simulations (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 5451-5459 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Molecular dynamics simulations of ionic systems require the inclusion of long-range electrostatic forces. We propose an expression for the long-range electrostatic forces based on an analytical solution of the Poisson–Boltzmann equation outside a spherical cutoff, which can easily be implemented in molecular simulation programs. An analytical solution of the linearized Poisson–Boltzmann (PB) equation valid in a spherical region is obtained. From this general solution special expressions are derived for evaluating the electrostatic potential and its derivative at the origin of the sphere. These expressions have been implemented for molecular dynamics (MD) simulations, such that the surface of the cutoff sphere around a charged particle is identified with the spherical boundary of the Poisson–Boltzmann problem. The analytical solution of the Poisson–Boltzmann equation is valid for the cutoff sphere and can be used for calculating the reaction field forces on the central charge, assuming a uniform continuum of given ionic strength beyond the cutoff. MD simulations are performed for a periodic system consisting of 2127 SPC water molecules with 40 NaCl ions (1 molar). We compare the structural and dynamical results obtained from MD simulations in which the long range electrostatic interactions are treated differently; using a cutoff radius, using a cutoff radius and a Poisson–Boltzmann generalized reaction field force, and using the Ewald summation. Application of the Poisson–Boltzmann generalized reaction field gives a dramatic improvement of the structure of the solution compared to a simple cutoff treatment, at no extra computational cost. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469273
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  • 9
    Electronic Resource
    Electronic Resource
    Predictions of free energy differences from a single simulation of the initial state (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 577-585 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have investigated the feasibility of using higher derivatives of the free energy, with respect to a coupling parameter λ, for predicting free energy changes between different states from a single simulation corresponding to the initial state, i.e., λ=0 in the normal thermodynamic integration approach. Terms up to and including the fifth derivative have been used. For a diatomic with point charges (dipole moment=2.4 D) in a box of water, the free energy corresponding to charge rearrangements of the order of ±0.25e could be predicted accurately after 750 ps of simulation and inclusion of the third derivative. Predictions were best for small perturbations. After 1000 ps of simulation, the first, second, third, and probably the fourth derivatives had converged, while the fifth was still oscillating. The possibility of predicting a multitude of free energy changes from a single simulation is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466975
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  • 10
    Electronic Resource
    Electronic Resource
    Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 3169-3174 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The dielectric constants (ε) of the simple point charge (SPC) and extended simple point charge (SPC/E) models of liquid water have been determined at 277 and 300 K using a reaction field (εRF) treatment for the long-range electrostatic interaction. Consistent dielectric constants are obtained by using statistical mechanical perturbation theory, such that the properties of the system correspond to εRF=ε, and are therefore representative of a true infinite system. The dielectric constants of SPC were determined to be 55.8 and 54.0 at 277 and 300 K, respectively, while the dielectric constants of SPC/E were 68.5 and 62.3 at 277 and 300 K, respectively.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466407
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