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  • 2005-2009  (124)
  • 1990-1994  (80)
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  • 1
    Electronic Resource
    Electronic Resource
    Reversible multiple time scale molecular dynamics (1992)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 1990-2001 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The Trotter factorization of the Liouville propagator is used to generate new reversible molecular dynamics integrators. This strategy is applied to derive reversible reference system propagator algorithms (RESPA) that greatly accelerate simulations of systems with a separation of time scales or with long range forces. The new algorithms have all of the advantages of previous RESPA integrators but are reversible, and more stable than those methods. These methods are applied to a set of paradigmatic systems and are shown to be superior to earlier methods. It is shown how the new RESPA methods are related to predictor–corrector integrators. Finally, we show how these methods can be used to accelerate the integration of the equations of motion of systems with Nosé thermostats.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.463137
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  • 2
    Electronic Resource
    Electronic Resource
    Density dependence of excess electronic ground-state energies in simple atomic fluids (1992)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 2002-2021 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The ground-state energies of an excess electron E0 as a function of solvent density are computed using model electron–atom pseudopotentials in fluid helium, argon, and xenon. E0 is a lower bound to the experimentally measurable threshold to photoconductivity, V0. The nonuniqueness of the pseudopotential description of electron–molecule interactions is demonstrated. We find that when many-body polarization effects are included, our calculated E0 results are in close agreement with experimental V0 values indicating that the conduction-band energy lies close to the ground-state energy across a broad range of densities in these polarizable fluids. If the many-body nature of the polarization interaction is ignored the ground-state energies deviate significantly from the V0 results highlighting the importance of accurate treatment of many-body polarization interactions. It is shown that a mean-field theory of polarization gives substantial agreement with full many-body calculations. This allows us to introduce a mean-field, density-dependent pair potential which greatly simplifies such many-body calculations. In the more polarizable systems, it is found that the spatial extent of the ground-state wave function as a function of solvent density is correlated with the density dependence of both V0 and the electron mobility, and it becomes uniformly spread throughout our simulation cell as the electron mobility goes through its maximum value at intermediate solvent densities.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.463138
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  • 3
    Electronic Resource
    Electronic Resource
    Many-body dispersion forces of polarizable clusters and liquids (1992)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 8628-8636 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A system of atoms with embedded Drude dispersion oscillators interacting through dipole–dipole forces is simulated. Using path integrals it is shown that after the coordinates of the dispersion oscillators are integrated out, the atoms interact through many-body dispersion forces to all orders of the dipole–dipole interaction. Simulations are carried out on clusters to see if the presence of many-body forces leads to ground state geometries different from those predicted from two-body potentials. In addition, the polarizability tensor of clusters is determined as a function of cluster size. Simulations are also carried out for fluids to see how many-body forces affect the pair correlation function. Lastly, the long-range interaction between van der Waals clusters is compared with the predictions of a summation over site–site two-body interactions. It is found that many-body forces have only a minor effect on the low energy geometries of van der Waals clusters, a somewhat surprising result given that many-body forces do give an important contribution to surface free energies of clusters and liquids. The vibrational frequencies of the breathing mode decrease by approximately 10%.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.463381
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  • 4
    Electronic Resource
    Electronic Resource
    Diffusion-limited reactions in spherical cavities (1992)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 96 (1992), S. 8840-8852 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We study a quenching reaction occurring at sinks within a spherical cavity and at the cavity surface. One may think of reactions at these two, distinct locations as two, coupled reactive channels. Reactions of the type D*+A→D+A are studied in the limit of nondilute A, present at both locations, and dilute D, present within the cavity. We use a Monte Carlo algorithm to compute mean rates, pseudo-first-order rates and branching ratios, and compare with results obtained by assuming that the two reactive channels operate in parallel. The ratio of activities of the two channels are varied; static and moving sinks are studied. We discuss an application to the determination of pore structure by NMR (nuclear magnetic resonance).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.462241
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  • 5
    Electronic Resource
    Electronic Resource
    Erratum: Molecular dynamics algorithm for multiple time scales: Systems with disparate masses [J. Chem. Phys. 94, 1465 (1991)] (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 7566-7566 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.460751
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  • 6
    Electronic Resource
    Electronic Resource
    Molecular dynamics algorithm for condensed systems with multiple time scales (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 1287-1291 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A frequently encountered problem in molecular dynamics simulations is the long runs required to study condensed systems consisting of both high frequency and low frequency degrees of freedom. Standard integrators require the choice of time step sufficiently small to guarantee stable solution of the highest frequency motion with the consequence that simulations require a very large number of central processing unit (CPU) cycles. In this note we present a new integrator that allows one to use a time step appropriate for the low frequency degrees of freedom without making any approximations related to the separation of time scales. This method is based on a choice of an analytically solvable reference system for the high frequency motion. We show how the analytical solution can be incorporated into a numerical integrator. The method is applied to two cases which are paradigms for this problem and it is shown that this approach and suitable generalizations should be very useful for future simulations of quantum and classical condensed matter systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.459140
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  • 7
    Electronic Resource
    Electronic Resource
    Monte Carlo methods for accelerating barrier crossing: Anti-force-bias and variable step algorithms (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 92 (1990), S. 1980-1985 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: For computer simulations of systems in which particles must cross large potential energy barriers, slow convergence is a problem. Basically there are two very disparate time scales: one characterizing motion in the potential wells and one characterizing the rare jumps from one stable well to another. Multiple time scale problems like this sorely test computer resources, and stand in the way of progress on simulations of chain folding, glass transitions, nucleation phenomena, activated barrier crossing, and quantum tunneling processes. Here several new methods are developed and tested on classical and quantum barrier crossings in double well problems. These new methods, called the anti-force-bias and variable step methods, lead to much faster convergence than standard methods. Convergence is tested by studying the deviation in the mean of the cumulative spatial distribution function from the exact distribution function.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.458029
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  • 8
    Electronic Resource
    Electronic Resource
    A new quantum propagator for hard sphere and cavity systems (1992)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 2382-2385 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new short time propagator for a particle interacting with a hard sphere or with a hard sphere cavity is derived. This new propagator is shown to be a much better approximation than the image approximations used in the literature and should prove useful for path integral or Green function Monte Carlo simulations. The simple example of the radial distribution function of a hard sphere gas is calculated using the new propagator as well as the older image approximation propagator and is shown to converge much more rapidly to the ab initio result.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.463076
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  • 9
    Electronic Resource
    Electronic Resource
    Comparison of rate theories for generalized Langevin dynamics (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 5809-5826 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Rate constants evaluated from (1) the energy-loss turnover theory of Pollak, Grabert, and Hänggi (PGH), (2) the Grote–Hynes extension of Kramers theory (GH), and (3) the microcanonical variational transition state theory for dissipative systems of Tucker and Pollak (μVTST) are compared with rate constants determined from direct computer simulations of generalized Langevin dynamics. The comparisons are made for a cubic oscillator under the influence of a slow bath characterized by a Gaussian friction kernel. In the μVTST calculations, which are based on an effective two degree of freedom Hamiltonian, barrier crossing due to energy transfer from the bath to the effective Hamiltonian is neglected. This neglect is significant only at very strong coupling, where it causes the μVTST results to drop below the simulation results. Both GH and μVTST theories fail (as expected) in the energy diffusion regime, while PGH theory is only moderately successful. The μVTST results agree extremely well with the simulation results in the spatial diffusion regime, providing a significant improvement over the GH results at intermediate coupling strengths and over the PGH results at strong coupling strengths. This improvement is a result of nonlinear effects which are included in the μVTST approach but neglected in the PGH and GH theories.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.461603
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  • 10
    Electronic Resource
    Electronic Resource
    Stochastic molecular dynamics in systems with multiple time scales and memory friction (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 4389-4396 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The generalized Langevin equation (GLE) has been used to model a wide variety of systems in which a subset of the degrees of freedom move on a potential of mean force surface subject to fluctuating forces and dynamic friction. When there is a wide separation in the time scales for motion on the potential surface and for relaxation of the friction kernel, direct integration of the GLE is very costly in CPU time. In this paper we introduce an integrator based on our previous work using numerical analytical propagator algorithm (NAPA) and reference system propagator algorithm (RESPA) that greatly accelerates such simulations. We also discuss sampling methods for the random force. Accuracy of this algorithm is assessed by comparisons with an analytically solvable example. Introducing dynamic friction kernels determined from full molecular dynamics (MD) simulations allows us to compare the accuracy of the GLE simulations with full scale molecular dynamics simulations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.461794
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