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  • 1990-1994  (9)
  • 1
    Electronic Resource
    Electronic Resource
    Brownian dynamics simulation of the superoxide-superoxide dismutase reaction: iron and manganese enzymes (1990)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 94 (1990), S. 959-961 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100365a084
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Multiconfiguration thermodynamic integration (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 1175-1188 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A modified thermodynamic integration technique is presented to obtain free energy differences from molecular dynamics simulations. In this multiconfiguration thermodynamic integration technique, the commonly employed single configuration (slow growth) approximation is not made. It is shown, by analysis of the sources of error, how the multiconfiguration variant of thermodynamic integration allows for a soundly based assessment of the statistical error in the evaluated free energy difference. Since ensembles of configurations are generated for each integration step, a statistical error can be evaluated for each integration step. By generating ensembles of different lengths, the statistical error can be equally distributed over the integration. This eliminates the difficult problem in single configuration thermodynamic integrations of determining the best rate of change of the Hamiltonian, which is usually based on equally distributing the free energy change. At the same time, this procedure leads to a more efficient use of computer time by providing the possibility of added accuracy from separate calculations of the same Hamiltonian change. The technique is applied to a simple but illustrative model system consisting of a monatomic solute in aqueous solution. In a second example, a combination of multiconfiguration thermodynamic integration and thermodynamic perturbation is used to obtain the potentials of mean force for rotation of the sidechain dihedral angles for valine and threonine dipeptides with restrained backbones in aqueous solution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.461148
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Inversion of receptor binding preferences by mutagenesis: Free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins (1993)
    s.l. : American Chemical Society
    Biochemistry 32 (1993), S. 7428-7434 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00080a013
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    Paper (German National Licenses)
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  • 4
    Electronic Resource
    Electronic Resource
    Treatment of rotational isomeric states. III. The use of biasing potentials (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 5032-5039 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A technique is described to determine umbrella biasing potentials that can be used to enhance sampling of rotational isomeric states in molecular simulations of polypeptides in water. The analytical biasing potential functions are obtained through fitting of potentials of mean force obtained by thermodynamic integration simulations to a small number of functions used to describe dihedral torsion. The resulting dramatic increase in efficiency of sampling is illustrated by comparison of molecular simulations of the alanine–dipeptide molecule in aqueous solution, with and without the use of the biasing potentials. The same biasing potentials were used in simulations of the alanine–tripeptide and the alanine–heptapeptide in aqueous solution. Similar dramatic increases in sampling efficiency were observed for these simulations, when the biasing potentials were applied, which suggests that these biasing potentials, although determined for the dipeptide, may be transferable to larger peptide chains. It is illustrated how the biasing potentials can be used in biasing potential annealing simulations, leading to rapid folding of peptide chains into aqueous solution structures with low energy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468409
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    Paper (German National Licenses)
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  • 5
    Electronic Resource
    Electronic Resource
    Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 9025-9031 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new method of simultaneously scaling and shifting the Lennard-Jones (LJ) potential in molecular dynamics (MD) and thermodynamic integration (TI) simulations is presented. The approach allows the smooth creation or annihilation of atoms or molecules in an ensemble of solvent molecules during a molecular simulation. By scaling and shifting the LJ potential in the direction of the interatomic distance between particles, the method eliminates the problem of the creation or annihilation of a large repulsive LJ potential at the initial or final state of a TI. The optimal degree of shifting and scaling the LJ potential as a function of a control variable λ was studied for the annihilation and creation of neon in aqueous solution. The method was further tested on the calculation of the free energy of aqueous solvation of a small molecule, ethanol. In contrast to linear scaling of the LJ potential during TI, the calculated free energies using the new separation-shifted scaling approach are reasonably well converged after 200–500 ps of simulation and show smaller hysteresis comparing forward and reverse TI.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466707
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    Paper (German National Licenses)
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  • 6
    Electronic Resource
    Electronic Resource
    Continuum model calculations of solvation free energies: accurate evaluation of electrostatic contributions (1992)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 96 (1992), S. 6428-6431 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100194a060
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    Paper (German National Licenses)
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  • 7
    Electronic Resource
    Electronic Resource
    Computational Alchemy (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physical Chemistry 43 (1992), S. 407-435 
    Details
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.pc.43.100192.002203
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    Paper (German National Licenses)
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  • 8
    Electronic Resource
    Electronic Resource
    Calculating electrostatic forces from grid-calculated potentials (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 401-409 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The accurate calculation of forces from finite difference potentials is very important, especially in the area of Brownian dynamics simulations. Test charge methods are typically used to calculate these forces. In these methods, the potential is calculated with one group of charges present, then the force on a second set of charges is calculated as the negative of the gradient of the potential times the charge. The test charge methods for calculating forces between solute molecules have been compared with more accurate methods and then regions of validity of the test charge methods explored. The test charge methods neglect certain reaction field effects. It is found for the simple charged systems studied that beyond a center-to-center separation of about twice the sum of the molecular radii the test charge approximations can be quite good. For polar molecules with no net charges, however, the corrections can be significant to even longer ranges.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110315
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    Paper (German National Licenses)
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  • 9
    Electronic Resource
    Electronic Resource
    ARGOS, a vectorized general molecular dynamics program (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 943-951 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The organization of the highly vectorizable molecular dynamics simulation program ARGOS is described. The specific choice of the data structure and the separation of the calculation of interactions involving solutes and solvent molecules allows a considerable improvement in computation speed. Illustrative results are given for the NEC SX-2/400 supercomputer. For the simulation of a large biological molecule in water a speedup factor of 5 is obtained as a result of vectorization of the code to 87%. The parts of the code used in a simulation of pure water could be vectorized to 98%, leading to an overall speedup factor due to vectorization of 13. The simulation of pure water runs over 300 times faster on the SX-2/400 than on the VAX 8650.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110806
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