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  • Articles  (5)
  • electrostatics  (5)
  • Wiley-Blackwell  (5)
  • 1995-1999  (5)
  • 1940-1944
  • Computer Science  (5)
  • 1
    Electronic Resource
    Electronic Resource
    ORAC: A Molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1848-1862 
    Details
    ISSN: 0192-8651
    Keywords: molecular dynamics ; biomolecules ; electrostatics ; software ; reversible multiple time-step algorithms ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this study, we present a new molecular dynamics program for simulation of complex molecular systems. The program, named ORAC, combines state-of-the-art molecular dynamics (MD) algorithms with flexibility in handling different types and sizes of molecules. ORAC is intended for simulations of molecular systems and is specifically designed to treat biomolecules efficiently and effectively in solution or in a crystalline environment. Among its unique features are: (i) implementation of reversible and symplectic multiple time step algorithms (or r-RESPA, reversible reference system propagation algorithm) specifically designed and tuned for biological systems with periodic boundary conditions; (ii) availability for simulations with multiple or single time steps of standard Ewald or smooth particle mesh Ewald (SPME) for computation of electrostatic interactions; and (iii) possibility of simulating molecular systems in a variety of thermodynamic ensembles. We believe that the combination of these algorithms makes ORAC more advanced than other MD programs using standard simulation algorithms.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1848-1862, 1997
    Additional Material: 2 Ill.
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    Paper (German National Licenses)
  • 2
    Electronic Resource
    Electronic Resource
    Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1591-1608 
    Details
    ISSN: 0192-8651
    Keywords: dielectric continuum ; Poisson-Boltzmann equation ; finite element ; electrostatics ; solvation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The automatic three-dimensional mesh generation system for molecular geometries developed in our laboratory is used to solve the Poisson-Boltzmann equation numerically using a finite element method. For a number of different systems, the results are found to be in good agreement with those obtained in finite difference calculations using the DelPhi program as well as with those from boundary element calculations using our triangulated molecular surface. The overall scaling of the method is found to be approximately linear in the number of atoms in the system. The finite element mesh structure can be exploited to compute the gradient of the polarization energy in 10-20% of the time required to solve the equation itself. The resulting timings for the larger systems considered indicate that energies and gradients can be obtained in about half the time required for a finite difference solution to the equation. The development of a multilevel version of the algorithm as well as future applications to structure optimization using molecular mechanics force fields are also discussed.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1591-1608, 1997
    Additional Material: 6 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1632-1646 
    Details
    ISSN: 0192-8651
    Keywords: force field ; electrostatics ; hydrogen bonding ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computational approach to the inclusion of off-center charges in both additive and nonadditive molecular mechanics calculations is presented. The additional sites in the molecular skeleton are placed in the approximate locations of the chemically intuitive electron lone pair, and are treated as formal particles throughout the calculation. The increase in the number of charge sites results in overall improvement in the energy associated with the angular dependence of hydrogen bonds and improved statistical accuracy of the electrostatic potential derived charges. The addition of lone pairs also results in improved accuracy in relative solvation free energy calculation for the pyridine to benzene and methanol to methane mutations. Because the number of atoms that require lone pairs is small, the extra accuracy can be achieved with little computational overhead.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1632-1646, 1997
    Additional Material: 3 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    Atomic radii: Incorporation of solvation effects (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1482-1493 
    Details
    ISSN: 0192-8651
    Keywords: atomic radii ; solute cavity ; solvation ; electrostatics ; solvent interaction potential ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic radii used to define the solute cavity in continuum-based methods are determined by reproducing the solvent-accessible surface defined as the loci of minima in a potential (solvent interaction potential) between the solute and a probe. This potential includes electrostatic interaction (ion-dipole, ion-quadrupole, and ion-induced dipole) terms as well as a Lennard-Jones energy term. The method alleviates the need to distinguish solute atoms in different chemical environments. These radii, when used in the calculation of solvation free energies, are shown to be superior to fixed atom-specific radii or to radii obtained from the electron isodensity surface from quantum-mechanical calculations.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1482-1493, 1998
    Additional Material: 2 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    Multi-multigrid solution of modified Poisson-Boltzmann equation for arbitrarily shaped molecules (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 893-901 
    Details
    ISSN: 0192-8651
    Keywords: Poisson-Boltzmann ; electrostatics ; Kirkwood ; Loeb ; multigrid ; multivalent ions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new multi-multigrid method is presented for solving the modified Poisson-Boltzmann equation based on the Kirkwood Hierarchy of equations, with Loeb's closure, on a three-dimensional grid. The results are compared with standard Poisson-Boltzmann calculations, which are known to underestimate the local concentration of counterions near charged parts of molecules, mainly due to neglect of fluctuations in the ionic concentrations. In the present study, the Kirkwood hierarchy of equations is discretized with the finite volume method and solved using multigrid techniques. The new possibility for solution of the three-dimensional modified Poisson-Boltzmann equation, for the first time within a model including a dielectric discontinuity, and within reasonable computational time, enables the calculation of higher valence ion distributions around arbitrarily shaped biological macromolecules.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 893-901, 1998
    Additional Material: 6 Ill.
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