Transition events in butane simulations: Similarities across models

From a variety of long simulations of all-atom butane using both stochastic and fully solved molecular dynamics, we have uncovered striking generic behavior that also occurs in one-dimensional systems. We find an apparently universal distribution of transition event durations, as well as a characteristic speed profile along the reaction coordinate. An approximate analytic distribution of event durations, derived from a one-dimensional model, correctly predicts the asymptotic behavior of the universal distribution for both short and long durations.

[1]  G. Voth,et al.  Reaction‐coordinate‐dependent friction in classical activated barrier crossing dynamics: When it matters and when it doesn’t , 1995 .

[2]  Dykman,et al.  Large fluctuations and fluctuational transitions in systems driven by colored Gaussian noise: A high-frequency noise. , 1990, Physical review. A, Atomic, molecular, and optical physics.

[3]  R. Pastor,et al.  Comparison of Langevin and molecular dynamics simulations. Equilibrium and dynamics of ethylene glycol in water , 1992 .

[4]  C. Dellago,et al.  Transition path sampling and the calculation of rate constants , 1998 .

[5]  D M Zuckerman,et al.  Efficient dynamic importance sampling of rare events in one dimension. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[6]  Thomas B. Woolf,et al.  Path corrected functionals of stochastic trajectories: towards relative free energy and reaction coordinate calculations , 1998 .

[7]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[8]  J. Andrew McCammon,et al.  Diffusive langevin dynamics of model alkanes , 1979 .

[9]  D. Luchinsky,et al.  Corrals and Critical Behavior of the Distribution of Fluctuational Paths. , 1996, Physical review letters.

[10]  M. Karplus,et al.  Stochastic boundary conditions for molecular dynamics simulations of ST2 water , 1984 .

[11]  Christoph Dellago,et al.  On the calculation of reaction rate constants in the transition path ensemble , 1999 .

[12]  Surmounting oscillating barriers: path-integral approach for weak noise , 2000, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[13]  P. Hänggi,et al.  Reaction rates when barriers fluctuate: A singular perturbation approach 1 Dedicated to the memory o , 1998 .

[14]  Stein,et al.  Symmetry breaking of fluctuation dynamics by noise color , 2000, Physical review letters.

[15]  Theory of activated rate processes: Coupled modes☆ , 1984 .

[16]  B. Brooks,et al.  Langevin dynamics of peptides: The frictional dependence of isomerization rates of N‐acetylalanyl‐N′‐methylamide , 1992, Biopolymers.

[17]  P. Hänggi,et al.  Reaction-rate theory: fifty years after Kramers , 1990 .

[18]  C. Gardiner.  Handbook of Stochastic Methods , 1983 .

[19]  Konrad Hinsen.  The molecular modeling toolkit: A new approach to molecular simulations , 2000 .

[20]  B. Berne,et al.  Numerical simulation of rate constants for a two degree of freedom system in the weak collision limit , 1987 .

[21]  Charles L. Brooks,et al.  The thermodynamics of solvophobic effects: A molecular‐dynamics study of n‐butane in carbon tetrachloride and water , 1990 .

[22]  Vadim N. Smelyanskiy,et al.  Resonant directed diffusion in nonadiabatically driven systems , 1998 .

[23]  G. Voth,et al.  Manifestations of spatially dependent friction in classical activated rate processes , 1993 .

[24]  Bruce J. Berne,et al.  A molecular dynamics and Monte Carlo study of solvent effects on the conformational equilibrium of n‐butane in CCl4a),b) , 1979 .

[25]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[26]  Vadim N. Smelyanskiy,et al.  Fluctuations, Escape, and Nucleation in Driven Systems: Logarithmic Susceptibility , 1997 .

[27]  T. Woolf,et al.  DYNAMIC REACTION PATHS AND RATES THROUGH IMPORTANCE-SAMPLED STOCHASTIC DYNAMICS , 1999 .

[28]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[29]  M. Karplus,et al.  Inertial effects in butane stochastic dynamics , 1989 .

[30]  The dependence of the potential of mean force on the solvent friction: Consequences for condensed phase activated rate theories , 1993 .