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  • 2005-2009  (124)
  • 1990-1994  (80)
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  • 11
    Electronic Resource
    Electronic Resource
    Molecular dynamics in systems with multiple time scales: Systems with stiff and soft degrees of freedom and with short and long range forces (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 8362-8364 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: When there are high and low frequency motions in systems with long and short range forces a judicious choice of reference system leads to very large accelerations in molecular dynamic (MD) simulations. Building on our previous work where we have developed reference system methods for systems with high frequency oscillators, disparate masses, or long range forces, we present a double reference system method which leads to acceleration of as much as 20 in systems consisting of 864 molecules with Lennard-Jones (12-6) forces. Much larger savings should be achieved when this method is applied to longer range forces and larger systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.461263
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  • 12
    Electronic Resource
    Electronic Resource
    Molecular dynamics algorithm for multiple time scales: Systems with disparate masses (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 1465-1469 
    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 mixtures of light and heavy particles. Standard methods require the choice of time step sufficiently small to guarantee stable solution for the low mass component with the consequence that these simulations require a very large number of central processing unit cycles to treat the relaxation of the heavier component. In this note, we present a new method that allows one to use a time step appropriate for the heavy particles. This method uses a similar idea to numerical analytical propogator algorithm, an algorithm we invented to treat high frequency oscillators interacting with low frequency baths and is based on a choice of a reference system for the light particle motions. The method is applied to the case of a liquid containing 864 Lennard-Jones spheres, 824 of these particles having a mass, M=100 and 40 spheres picked at random have a mass m=1. It is shown that molecular dynamics using the new algorithm runs seven to ten times faster than standard methods and this approach as well as 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/10.1063/1.460004
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  • 13
    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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  • 14
    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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  • 15
    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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  • 16
    Electronic Resource
    Electronic Resource
    Dynamic friction on rigid and flexible bonds (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 5084-5095 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A wide variety of problems involving molecular motion in liquids can be formulated in terms of the generalized Langevin equation (GLE). The friction coefficient on a molecular bond or on some more complicated reaction coordinate is then required. An often used approximation is to set the dynamic friction constant equal to the autocorrelation function of the fluctuating force exerted on the frozen bond by the remaining unfrozen coordinates. The true friction involves projection operators and should differ from this approximation. In this paper we derive various identities and show that the rigid bond approximation is the high frequency limit of the true dynamic friction coefficient. We compute the "true'' dynamic friction and the friction approximated on the basis of the rigid or frozen bond and show that the asymptotic limit is very accurate even for frequencies not much larger than the peak frequency of the solvent spectral density. Two different dynamical systems are studied using MD simulations with our newly devised NAPA integrator for systems with disparate time scales. In one the molecule is not allowed to rotate and in the other it is allowed to rotate. Interestingly, even for very long rotational reorientation times, small but significant differences in the long time decay of the bond dynamic friction are observed for rotational and nonrotational molecules—differences, however, that do not produce large differences in the static friction constants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.458647
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  • 17
    Electronic Resource
    Electronic Resource
    Method for accelerating chain folding and mixing (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 6071-6077 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: An algorithm based on allowing the form of the intermolecular potential to fluctuate is introduced into molecular dynamics and Monte Carlo simulations. It is shown that this method accelerates the approach to equilibrium in frustrated systems. It provides a very useful method for determining all of the local minima in complex systems. Examples are mixing in dense binary liquids and folding of long polymer chains. When this method is combined with umbrella sampling techniques it accelerates the simulations of a wide class of chemically important systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.465904
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  • 18
    Electronic Resource
    Electronic Resource
    A Born–Oppenheimer approximation for path integrals with an application to electron solvation in polarizable fluids (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 2902-2916 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The Born–Oppenheimer approximation is introduced into the path integral expression for the canonical partition function. It is difficult to apply this to simulations. We devise a new adiabatic expression which we call the free energy Born–Oppenheimer approximation which is much easier to simulate. It is shown that this approximation deviates from the exact path-integral expression by no more than does the standard Born–Oppenheimer approximation and we apply it to the problem of an excess electron dissolved in a polarizable fluid.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.465198
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  • 19
    Electronic Resource
    Electronic Resource
    Reply to Comment on: Reversible multiple time scale molecular dynamics (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 2278-2279 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In response to the comment by Toxvaerd [J. Chem. Phys. 99, XXX (1993)], it is shown that two simple integrators, position Verlet and velocity Verlet, derived as introductory examples give rise to distinct trajectories. Leap-frog forms are derived for the integrators and using operator algebra the true relationship between the two trajectories are determined. The trajectories do not diverge as a function of time but mirror each other. This was not pointed out in the original paper but it is presented here in response to the comment. The simpler analysis of the Toxvaerd comment does not correctly define this relationship and incorrectly implies that the two methods generate identical trajectories.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.465242
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  • 20
    Electronic Resource
    Electronic Resource
    Theory of polarizable liquid crystals: Optical birefringence (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 2213-2220 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The theory of polarizable anisotropic fluids is developed on the basis of a model fluid consisting of anisotropic Drude oscillators with embedded permanent dipoles. A matrix theory is developed. The dielectric tensor is derived and a matrix Monte Carlo method is used to calculate the optical absorption and birefringence of ordered fluids.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466200
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