TY - JOUR
T1 - Transition pathways in complex systems
T2 - Application of the finite-temperature string method to the alanine dipeptide
AU - Ren, Weiqing
AU - Vanden-Eijnden, Eric
AU - Maragakis, Paul
AU - E, Weinan
N1 - Funding Information:
The authors thank M. Karplus for helpful discussions. Two of the authors (W. E) and (E. V.-E.) were partially supported by ONR Grant Nos. N00014-01-1-0674 and N00014-04-1-0565, and NSF Grant Nos. DMS01-01439, DMS02-09959, and DMS02-39625. Another author (P.M.) acknowledges support by the Marie Curie European Fellowship Grant No. MEIF-CT-2003-501953. The explicit water calculations were performed in the Crimson Grid cluster at Harvard, the SDSC teragrid and the CIMS computer center.
PY - 2005/10/3
Y1 - 2005/10/3
N2 - 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.
AB - 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.
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U2 - 10.1063/1.2013256
DO - 10.1063/1.2013256
M3 - Review article
C2 - 16223277
AN - SCOPUS:33746187786
SN - 0021-9606
VL - 123
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
IS - 13
M1 - 134109
ER -