A novel protocol for simulation of highly viscous molecular systems

摘要

Computer simulation of viscous materials, such as bulk polymers or self-assembled two-dimensional films, are often required to produce meaningful structure-property relationships for such systems. Current constraints on computational resources restrict typical Molecular Dynamics (MD) simulations to time scales much shorter than the relevant relaxation times for these materials. We have characterized the performance of a new algorithm, called Protracted Colored-Noise Dynamics, to efficiently sample phase space for such viscous systems. The algorithm significantly reduced the Mean First Passage Time for a one-dimensional double-well oscillator. This algorithm appears to work because it locally increases the entropy of the conformational transition state.