Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide

Weiqing Ren, Eric Vanden Eijnden, Paul Maragakis, Weinan E

Research output: Contribution to journalArticle

Abstract

The finite-temperature string method proposed by E, [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002)] is a very effective way of identifying transition mechanisms and transition rates between metastable states in systems with complex energy landscapes. In this paper, we discuss the theoretical background and algorithmic details of the finite-temperature string method, as well as the application to the study of isomerization reaction of the alanine dipeptide, both in vacuum and in explicit solvent. We demonstrate that the method allows us to identify directly the isocommittor surfaces, which are approximated by hyperplanes, in the region of configuration space where the most probable transition trajectories are concentrated. These results are verified subsequently by computing directly the committor distribution on the hyperplanes that define the transition state region.

Original languageEnglish (US)
Article number134109
JournalJournal of Chemical Physics
Volume123
Issue number13
DOIs
StatePublished - Oct 3 2005

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Dipeptides
alanine
complex systems
Alanine
Large scale systems
strings
hyperplanes
Isomerization
Trajectories
Vacuum
Temperature
temperature
metastable state
isomerization
trajectories
vacuum
configurations
energy

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Transition pathways in complex systems : Application of the finite-temperature string method to the alanine dipeptide. / Ren, Weiqing; Vanden Eijnden, Eric; Maragakis, Paul; E, Weinan.

In: Journal of Chemical Physics, Vol. 123, No. 13, 134109, 03.10.2005.

Research output: Contribution to journalArticle

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