Abstract
Algorithmic improvements of the dimer method [G. Henkelman and H. Jónsson, J. Chem. Phys. 111, 7010 (1999)] are described in this paper. Using the limited memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) optimizer for the dimer translation greatly improves the convergence compared to the previously used conjugate gradient algorithm. It also saves one energy and gradient calculation per dimer iteration. Extrapolation of the gradient during repeated dimer rotations reduces the computational cost to one gradient calculation per dimer rotation. The L-BFGS algorithm also improves convergence of the rotation. Thus, three to four energy and gradient evaluations are needed per iteration at the beginning of a transition state search, while only two are required close to convergence. Moreover, we apply the dimer method in internal coordinates to reduce coupling between the degrees of freedom. Weighting the coordinates can be used to apply chemical knowledge about the system and restrict the transition state search to only part of the system while minimizing the remainder. These improvements led to an efficient method for the location of transition states without the need to calculate the Hessian. Thus, it is especially useful in large systems with expensive gradient evaluations.
References
30
Referenced
358
10.1063/1.1749604/ J. Chem. Phys. (1935)10.1039/tf9353100875/ Trans. Faraday Soc. (1935)10.1063/1.1323224/ J. Chem. Phys. (2000)10.1142/9789812839664_0016/ Classical and Quantum Dynamics in Condensed Phase Simulations (1998)10.1063/1.1329672/ J. Chem. Phys. (2000)10.1063/1.1691018/ J. Chem. Phys. (2004)10.1103/PhysRevB.66.052301/ Phys. Rev. B (2002)10.1063/1.442352/ J. Chem. Phys. (1981)10.1021/j100238a013/ J. Phys. Chem. (1983)10.1021/j100247a015/ J. Phys. Chem. (1985)10.1002/jcc.540070402/ J. Comput. Chem. (1986)10.1063/1.2104507/ J. Chem. Phys. (2005)10.1063/1.480097/ J. Chem. Phys. (1999)10.1063/1.1809574/ J. Chem. Phys. (2004){'key': '2023080205345596400_c15'}10.1016/s0166-1280(03)00285-9/ J. Mol. Struct.: THEOCHEM (2003){'key': '2023080205345596400_c17'}10.1080/00268970512331340592/ Mol. Phys. (2005){'key': '2023080205345596400_c19'}10.1007/BF01589116/ Math. Program. (1989)10.2307/2006193/ Math. Comput. (1980)10.1063/1.462844/ J. Chem. Phys. (1992)10.1002/(SICI)1096-987X(19960115)17:1<49::AID-JCC5>3.0.CO;2-0/ J. Comput. Chem. (1996)10.1039/a909486e/ Phys. Chem. Chem. Phys. (2000)10.1002/(SICI)1096-987X(199706)18:8<1079::AID-JCC12>3.0.CO;2-8/ J. Comput. Chem. (1997)10.1002/(SICI)1096-987X(199605)17:7<888::AID-JCC12>3.0.CO;2-7/ J. Comput. Chem. (1996)10.1021/ja00299a024/ J. Am. Chem. Soc. (1985){'volume-title': 'Biomolecular Simulation: The GROMOS96 Manual and User Guide', 'year': '1996', 'key': '2023080205345596400_c28'}/ Biomolecular Simulation: The GROMOS96 Manual and User Guide (1996)10.1021/ct050252w/ J. Chem. Theory Comput. (2006)10.1021/ct049844p/ J. Chem. Theory Comput. (2005)
Dates
| Type | When |
|---|---|
| Created | 17 years, 7 months ago (Jan. 7, 2008, 6:18 p.m.) |
| Deposited | 2 years, 1 month ago (Aug. 2, 2023, 1:35 a.m.) |
| Indexed | 44 minutes ago (Sept. 7, 2025, 5:54 p.m.) |
| Issued | 17 years, 8 months ago (Jan. 7, 2008) |
| Published | 17 years, 8 months ago (Jan. 7, 2008) |
| Published Online | 17 years, 8 months ago (Jan. 7, 2008) |
| Published Print | 17 years, 8 months ago (Jan. 7, 2008) |
@article{K_stner_2008, title={Superlinearly converging dimer method for transition state search}, volume={128}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.2815812}, DOI={10.1063/1.2815812}, number={1}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Kästner, Johannes and Sherwood, Paul}, year={2008}, month=jan }