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  • 1
    Electronic Resource
    Electronic Resource
    An efficient newton-like method for molecular mechanics energy minimization of large molecules (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1016-1024 
    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: Techniques from numerical analysis and crystallographic refinement have been combined to produce a variant of the Truncated Newton nonlinear optimization procedure. The new algorithm shows particular promise for potential energy minimization of large molecular systems. Usual implementations of Newton's method require storage space proportional to the number of atoms squared (i.e., O(N2)) and computer time of O(N3). Our suggested implementation of the Truncated Newton technique requires storage of less than O(N1.5) and CPU time of less than O(N2) for structures containing several hundred to a few thousand atoms. The algorithm exhibits quadratic convergence near the minimum and is also very tolerant of poor initial structures. A comparison with existing optimization procedures is detailed for cyclohexane, arachidonic acid, and the small protein crambin. In particular, a structure for crambin (662 atoms) has been refined to an RMS gradient of 3.6 × 10-6 kcal/mol/Å per atom on the MM2 potential energy surface. Several suggestions are made which may lead to further improvement of the new method.
    Additional Material: 5 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080710
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  • 2
    Electronic Resource
    Electronic Resource
    Geometrical and spectroscopical characterizations of some complex entities of aluminum(III) with fluoride ions by LDF-based calculations (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 927-934 
    Details
    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: The structure of cryolite is investigated with a theoretical approach based on LDF calculations. In fact, experimental techniques for structural studies are difficult to perform in cryolite melts because of hard experimental conditions (high temperature, corrosiveness, etc.). Use of the DMol software allows us to determine the stabilities and the vibrational frequencies of AlF63-, AlF52-, and AlF4- isolated complexes. The results obtained compared with published experimental works confirm that AlF52- should be considered in the dissociation scheme of cryolite as previously evidenced by other authors. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520418
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 402-409 
    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: A numerical method for calculating the volume of a macromolecule and its first and second derivatives as a function of atomic coordinates is presented. For N atoms, the method requires about 0.3 N ln(N) seconds of CPU time on a VAX-8800 to evaluate the volume and derivatives. As a test case, the method was used to evaluate a pressure-volume energy term in energy minimizations of the protein lysozyme at 1000 atm (1 atm = 1.013 × 105 Pa). R.m.s. gradients of 10-4 kcal/mol/Å were obtained at convergence. The calculated structures exhibited pressure-induced changes which were qualitatively similar to the changes observed in the 1000 atm structure determined by X-ray crystallography.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540120314
    Library Location Call Number Volume/Issue/Year Availability
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    Paper (German National Licenses)
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