A General Long-Time Molecular Dynamics Scheme in Atomistic Systems: Hyperdynamics in Entropy Dominated Systems

We extend the hyperdynamics method developed for low-dimensional energy-dominated systems, to simulate slow dynamics in more general atomistic systems. We show that a few functionals of the pair distribution function forms a low-dimensional collective space, which is a good approximation to distinguish stable and transitional conformations. A bias potential that raises the energy in stable regions, where the system is at local equilibrium, is constructed in the pair-correlation space on the fly. Thus a new MD scheme is present to study any time-scale dynamics with atomic details. We examine the slow gas-liquid transition of Lennard-Jones systems and show that this method can generate correct long-time dynamics and focus on the transition conformations without prior knowledge of the systems. We also discuss the application and possible improvement of the method for more complex systems.

[1]  John W. Wilkins,et al.  Simple bias potential for boosting molecular dynamics with the hyperdynamics scheme , 1998 .

[2]  A. Voter.  A method for accelerating the molecular dynamics simulation of infrequent events , 1997 .

[3]  J. Tully,et al.  Puddle-skimming: An efficient sampling of multidimensional configuration space , 2002 .

[4]  Kurt Kremer,et al.  Hyperdynamics for entropic systems: time-space compression and pair correlation function approximation. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[5]  Ron Elber,et al.  Calculation of classical trajectories with a very large time step: Formalism and numerical examples , 1996 .

[6]  Evans,et al.  Direct entropy calculation from computer simulation of liquids. , 1989, Physical review. A, General physics.

[7]  Ron Elber,et al.  Long-timescale simulation methods. , 2005, Current opinion in structural biology.

[8]  Giaquinta,et al.  Entropy and the freezing of simple liquids. , 1992, Physical review. A, Atomic, molecular, and optical physics.

[9]  H. S. Green.  The molecular theory of fluids , 1970 .

[10]  R. Miron,et al.  Accelerated molecular dynamics with the bond-boost method , 2003 .

[11]  David Chandler,et al.  Transition path sampling: throwing ropes over rough mountain passes, in the dark. , 2002, Annual review of physical chemistry.

[12]  A. B. Bortz,et al.  A new algorithm for Monte Carlo simulation of Ising spin systems , 1975 .

[13]  Christoph Dellago,et al.  Transition path sampling: throwing ropes over mountains in the dark , 2000 .

[14]  Donald Hamelberg,et al.  Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis. , 2005, Journal of the American Chemical Society.