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

Fingerprint

Fluxes
Adenosine
Molecular dynamics
adenosines
Trajectories
Data storage equipment
trajectories
molecular dynamics
approximation
energy

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Revisiting and computing reaction coordinates with directional milestoning. / Kirmizialtin, Serdal; Elber, Ron.

In: Journal of Physical Chemistry A, Vol. 115, No. 23, 16.06.2011, p. 6137-6148.

Research output: Contribution to journalArticle

@article{ecf65809a05646a68cee90cb3b54b7d1,
title = "Revisiting and computing reaction coordinates with directional milestoning",
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.",
author = "Serdal Kirmizialtin and Ron Elber",
year = "2011",
month = "6",
day = "16",
doi = "10.1021/jp111093c",
language = "English (US)",
volume = "115",
pages = "6137--6148",
journal = "Journal of Physical Chemistry A",
issn = "1089-5639",
publisher = "American Chemical Society",
number = "23",

}

TY - JOUR

T1 - Revisiting and computing reaction coordinates with directional milestoning

AU - Kirmizialtin, Serdal

AU - Elber, Ron

PY - 2011/6/16

Y1 - 2011/6/16

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=79959945891&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79959945891&partnerID=8YFLogxK

U2 - 10.1021/jp111093c

DO - 10.1021/jp111093c

M3 - Article

VL - 115

SP - 6137

EP - 6148

JO - Journal of Physical Chemistry A

JF - Journal of Physical Chemistry A

SN - 1089-5639

IS - 23

ER -