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  • Biochemistry  (5)
  • Wiley-Blackwell  (5)
  • American Chemical Society
  • Springer Nature
  • 1990-1994  (5)
  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 606-610 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Geometry optimization directly in Cartesian coordinates using the EF and GDIIS algorithms with standard Hessian updating techniques is compared and contrasted with optimization in internal coordinates utilizing the well known Z-matrix formalism. Results on a test set of 20 molecules show that, with an appropriate initial Hessian, optimization in Cartesians is just as efficient as optimization in internals, thus rendering it unnecessary to construct a Z-matrix in situations where Cartesians are readily available, for example from structural databases or graphical model builders.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 838-846 
    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 detailed comparison has been made of the performance of molecular dynamics and hybrid Monte Carlo simulation algorithms for calculating thermodynamic properties of 2D Lennard-Jonesium. The hybrid Monte Carlo simulation required an order of magnitude fewer steps than the molecular dynamics simulation to calculate reproducible values of the specific heat. The ergodicity of the two algorithms was compared via the use of intermediate scattering functions. For classical systems the intermediate scattering functions should be real; however, a simple analysis demonstrates that this function will have a significant imaginary component when ergodicity breaks down. For q vectors near the zone boundary, the scattering functions are real for both algorithms. However, for q vectors near the zone center (i.e., harmonic, weakly coupled modes), the scattering function calculated via molecular dynamics had a significantly larger imaginary component than that calculated using hybrid Monte Carlo. Therefore, the hybrid Monte Carlo algorithm is more ergodic and samples phase space more efficiently than molecular dynamics for simulations of 2D Lennard-Jonesium. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1339-1346 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Modifications are made to a previously published algorithm for constrained optimization in Cartesian coordinates (J. Comp. Chem., 13, 240, 1992) to incorporate both fixed and dummy atoms. Standard distance and angle constraints can now be specified with respect to dummy atoms, greatly extending the range of constraints that can be handled. Fixed atoms can be eliminated from the optimization space and so there is no need to calculate their gradients resulting in potentially significant savings of CPU time in ab initio computations. Several examples illustrate the range and versatility of the modified algorithm. © John Wiley & Sons, Inc.
    Additional Material: 2 Tab.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 240-253 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient algorithm for constrained geometry optimization in Cartesian coordinates is presented. It incorporates mode-following techniques within both the classical method of Lagrange multipliers and the penalty function method. Both constrained minima and transition states can be located and, unlike the standard Z-matrix using internal coordinates, the desired constraints do not have to be satisfied in the initial structure. The algorithm is as efficient as a Z-matrix optimization while presenting several additional advantages.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1085-1100 
    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 comparison is made between geometry optimization in Cartesian coordinates, using an appropriate initial Hessian, and natural internal coordinates. Results on 33 different molecules covering a wide range of symmetries and structural types demonstrate that both coordinate systems are of comparable efficiency. There is a marked tendency for natural internals to converge to global minima whereas Cartesian optimizations converge to the local minimum closest to the starting geometry. Because they can now be generated automatically from input Cartesians, natural internals are to be preferred over Z-matrix coordinates. General optimization strategies using internal coordinates and/or Cartesians are discussed for both unconstrained and constrained optimization. © John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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