Revisiting and computing reaction coordinates with directional milestoning

Research output: Contribution to journalArticle

Abstract

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 languageEnglish (US)
Pages (from-to)6137-6148
Number of pages12
JournalJournal of Physical Chemistry A
Volume115
Issue number23
DOIs
StatePublished - Jun 16 2011

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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