J Phys Chem B. 2016 Aug 25;120(33):8600-5. doi: 10.1021/acs.jpcb.6b02654. Epub 2016 Jun 06.

Reaction Coordinate-Free Approach to Recovering Kinetics from Potential-Scaled Simulations: Application of Kramers' Rate Theory.

The journal of physical chemistry. B

Aaron T Frank, Ioan Andricioaei

PMID: 27220565 DOI: 10.1021/acs.jpcb.6b02654

Abstract

Enhanced sampling techniques are used to increase the frequency of "rare events" during computer simulations of complex molecules. Although methods exist that allow accurate thermodynamics to be recovered from enhanced simulations, recovering kinetics proves to be more challenging. Here we present an extrapolation approach that allows reliable kinetics to be recovered from potential-scaled MD simulations. The approach, based on Kramers' rate theory, is simple and computationally efficient, and allows kinetics to be recovered without defining reaction coordinates. To test our approach, we use it to determine the kinetics of barrier crossing between two metastable states on the 2D-Müller potential and the C7eq to αR transition in alanine dipeptide. The mean first passage time estimates obtained are in excellent agreement with reference values obtained from direct simulations on the unscaled potentials performed over times that are orders of magnitude longer.

Publication Types

• Journal Article
• Research Support, U.S. Gov't, Non-P.H.S.

Grant support

• T34 GM008078/GM/NIGMS NIH HHS/United States