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  • 1
    Electronic Resource
    Electronic Resource
    The Aqueous Solvation of Water: A Comparison of Continuum Methods with Molecular Dynamics (1994)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 116 (1994), S. 3949-3954 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00088a034
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  • 2
    Electronic Resource
    Electronic Resource
    Carboxypeptidase Y-catalyzed transpeptidation of esterified oligo- and polypeptides and its use for the specific carboxyl-terminal labeling of proteins (1992)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 114 (1992), S. 2603-2610 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00033a037
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  • 3
    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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  • 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
    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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  • 9
    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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  • 10
    Electronic Resource
    Electronic Resource
    Dynamical fluctuating charge force fields: Application to liquid water (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 6141-6156 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new molecular dynamics model in which the point charges on atomic sites are allowed to fluctuate in response to the environment is developed and applied to water. The idea for treating charges as variables is based on the concept of electronegativity equalization according to which: (a) the electronegativity of an atomic site is dependent on the atom's type and charge and is perturbed by the electrostatic potential it experiences from its neighbors and (b) charge is transferred between atomic sites in such a way that electronegativities are equalized. The charges are treated as dynamical variables using an extended Lagrangian method in which the charges are given a fictitious mass, velocities, and kinetic energy and then propagated according to Newtonian mechanics along with the atomic degrees of freedom. Models for water with fluctuating charges are developed using the geometries of two common fixed-charge water potentials: the simple point charge (SPC) and the four-point transferable intermolecular potential (TIP4P). Both fluctuating charge models give accurate predictions for gas-phase and liquid state properties, including radial distribution functions, the dielectric constant, and the diffusion constant. The method does not introduce any new intermolecular interactions beyond those already present in the fixed charge models and increases the computer time by only a factor of 1.1, making this method tractable for large systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468398
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