The method of Directional Milestoning is revisited. We start from an exact and more general expression and state the conditions and validity of the memory-loss approximation. An algorithm to compute a reaction coordinate from Directional Milestoning data is presented. The reaction coordinate is calculated as a set of discrete jumps between Milestones that maximizes the flux between two stable states. As an application we consider a conformational transition in solvated adenosine. We compare a long molecular dynamic trajectory with Directional Milestoning and discuss the differences between the maximum flux path and minimum energy coordinates.
|Original language||English (US)|
|Number of pages||12|
|Journal||Journal of Physical Chemistry A|
|State||Published - Jun 16 2011|
ASJC Scopus subject areas
- Physical and Theoretical Chemistry