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  • 1
    Electronic Resource
    Electronic Resource
    Molecular dynamics algorithm for multiple time scales: Systems with long range forces (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 6811-6815 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A frequently encountered problem in molecular dynamics is how to treat the long times that are required to simulate condensed systems consisting of particles interacting through long range forces. Standard methods require the calculation of the forces at every time step. Because each particle interacts with all particles within the interaction range of the potential the longer the range of the potential the larger the number forces that must be calculated at each time step. In this note we present a variant of the RESPA (reference system propagator algorithm), which we developed for handling systems with multiple time scales like disparate mass mixtures. This version of RESPA greatly reduces the number of forces that must be computed at each time step and thereby leads to a dramatic acceleration of such simulations. The RESPA method uses ideas similar to NAPA, an algorithm we invented to treat high frequency oscillators interacting with low frequency bath. The method is based on a choice of a reference system in which the particles interact through short range forces. The reference system is numerically integrated for n time steps δt and the error incurred by using short range forces is corrected by solving a rigorous set of equations once every Δt=nδt. This method reduces the cpu time dramatically. 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/10.1063/1.460259
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  • 2
    Electronic Resource
    Electronic Resource
    Erratum: Energy diffusion in many-dimensional Markovian systems. The consequences of competition between inter- and intramolecular vibrational energy transfer [J. Chem. Phys. 85, 2999 (1986)] (1987)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 86 (1987), S. 5223-5223 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.452788
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  • 3
    Electronic Resource
    Electronic Resource
    Numerical simulation of rate constants for a two degree of freedom system in the weak collision limit (1987)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 86 (1987), S. 4296-4297 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.451890
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  • 4
    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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  • 5
    Electronic Resource
    Electronic Resource
    Spatial dependence of time-dependent friction for pair diffusion in a simple fluid (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 6804-6812 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Molecular dynamics simulations are used to determine the time-dependent friction for pair diffusion in an isotropic Lennard-Jones fluid as a function of the separation between two diffusing particles. A numerical method proposed by Straub, Borkovec and Berne is used. It is found that both the initial value and the detailed time-dependence of the friction are dependent on the interparticle separation. The dependence of the pair diffusion coefficient on separation is determined. Comparisons are made with various hydrodynamic and collision theories. The rate constant for diffusion controlled reactions is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.458950
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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
    Low-temperature variational approximation for the Feynman quantum propagator and its application to the simulation of quantum systems (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 92 (1990), S. 7531-7539 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The low-temperature propagator of Mak and Andersen [J. Chem. Phys. 92, 2953 (1990)] allows for much more rapid convergence of Feynman path integral computer simulations of quantum systems. The effectiveness of this propagator is very sensitive to the choice of an effective frequency and the choice of this made by Mak and Andersen, although good, is not optimum. In this paper a harmonic reference system is used together with a variation principle to compute this effective frequency. Simulations show that when this is used in the low temperature propagator, the results converge much more rapidly than for other choices of the frequency. Moreover, an energy estimator is derived, which allows this effective potential to be used for the determination of the energy of the quantum system. In addition, using a cumulant expansion of the centroid density in the free particle reference system, an effective potential along with a corresponding energy estimator is derived and compared to the above.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.458189
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  • 8
    Electronic Resource
    Electronic Resource
    On energy estimators in path integral Monte Carlo simulations: Dependence of accuracy on algorithm (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 6359-6366 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Two energy estimators, the Barker estimator and the Berne virial estimator, commonly used in path integral simulations of quantum systems are compared with respect to statistical accuracy. It is found that the accuracy of these estimators is strongly affected by the algorithm used. Four common algorithms are considered here: (1) the pure primitive algorithm, (2) the primitive algorithm augmented by whole chain moves, (3) the normal-mode algorithm, and (4) the staging algorithm. The error of the mean of the Barker energy estimator is found to grow as (P)1/2, where P is the number of discretization points of the quantum paths (or the number of chain particles in the isomorphic classical chain), for all of the algorithms above. The error of the mean of the Berne virial energy estimator is independent of P for algorithms 2, 3, and 4, and increases as (P)1/2 for algorithm 1. It is concluded that the virial estimator is far more accurate than the Barker estimator for algorithms 2, 3, and 4, and is at least as accurate for algorithm 1. Because the error analysis depends strongly on the temporal correlations in the sequence of values of the energy estimator generated during Monte Carlo or molecular-dynamics simulations, we review the general question of error analysis in simulations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.457403
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  • 9
    Electronic Resource
    Electronic Resource
    Molecular dynamics study of an isomerizing diatomic in a Lennard-Jones fluid (1988)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 89 (1988), S. 4833-4847 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The behavior of the reaction rate of an isomerizing diatomic molecule solvated in a Lennard-Jones fluid is studied by molecular dynamics simulations. A comprehensive study of solvation effects on the rate constant, using the reactive flux absorbing boundary approximation of Straub and Berne, is presented. We provide simulation data over three orders of magnitude in solvent density for four systems differing in the mass of the solvent atoms and frequencies of the internal potential. Rate constants are also calculated for the model system using both Langevin Dynamics with exponential memory and impulsive collision dynamics of the BGK model. A simple method for calculating the average energy transfer and collision frequency is used to determine the collision efficiency for systems in which the mass of the solvent atoms is lighter than, equal to, or heavier than that of the atoms composing the isomerizing diatomic. We find that for solvents of equal and heavy mass compared to the solute the impulsive collision model provides the best description of the dynamics. Finally, we employ a method recently introduced by us to calculate the spatial dependence of the dynamic friction; we compare the reaction coordinate friction at the transition state separation with an approximation based on the single particle friction. This directly calculated reaction coordinate friction, when combined with the Grote–Hynes theory for barrier crossing, gives good agreement with the simulation data at high density.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.455678
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  • 10
    Electronic Resource
    Electronic Resource
    Structure and energetics of Xe−n (1988)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 88 (1988), S. 4516-4525 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Diffusion Monte Carlo simulations were performed to determine the absolute binding energies of an excess electron to small clusters of xenon atoms (n≤19). It was found that clusters as small as Xe6 could bind the electron. The ground state wave function of the excess electron and the decomposition of the binding energy of the electron into kinetic and potential parts were determined for a number of small clusters. Large (n〉50) and small clusters anions were then studied at finite temperatures using path integral Monte Carlo. In all cases the excess electron in small clusters was found to exist in very diffuse state extending well beyond the radius of the cluster. However, in large clusters the electron was localized within the bulk of the cluster. Various properties are presented to characterize the electron in Xe−n as function of cluster size and the results compared to an electron solvated in fluid xenon.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.453759
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