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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 9283-9290 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new Monte Carlo sampling scheme which estimates the shape of an energy hypersurface as a covariance tensor to generate variable Monte Carlo steps, is developed. The feasibility of this method is tested on 256 Lennard-Jones particles at T*=0.719, ρ*=0.85, and 216 TIP4P water molecules at T=298 K and the results are compared with those of other methods. It is found that the Lennard-Jones solid is successfully melted to liquid by the new method while it is failed by the Metropolis algorithm and the radial distribution functions correspond well to those of other established methods. The result shows that the new method has very improved features in several respects. First, the convergence property to reach the equilibrium state is better than that of other methods. Secondly, the equilibrium distribution of ensembles are not biased.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: High-directional Monte Carlo (HDMC) simulations are performed to investigate the behavior of water molecules in the catalytic sites of human ras p21 proteins and the results are compared among three types of hydrated ras p21 proteins: the normal ras complexed with GDP (normal-p21/GDP), the mutant ras complexed with GDP (mutant-p21/GDP), and the normal ras complexed with GTP (normal-p21/GTP). Also, the original Metropolis Monte Carlo (MMC) simulation is performed on the normal-p21/GDP system. Comparison between HDMC and MMC shows the improved efficeincy of HDMC on this complicated system. Interaction between water molecules is represented by the TIP3P potential function. The solute-water interaction is represented by the Coulomb and van der Waals interactions from the CHARMM force field spliced with TIP3P. The mean-square displacements and dipole correlation functions are reported. We specifically examined the hydrogen-bond interactions existing near the catalytic sites, by the distribution of small water clusters connected by the hydrogen bond and by the average lengths and fluctations of hydrogen bonds between water molecules and solute atoms. Water molecules form different local structures in different types of the p21/GDP(GTP) complexes. The structure and motion of water molecules near the catalytic sites of the proteins are discussed in detail. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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