Deep learning-based initial guess for minimum energy path calculations

Hyunsoo Park; Sangwon Lee; Jihan Kim

Korean Journal of Chemical Engineering, Vol.38, No.2, 406-410, February, 2021

DOI10.1007/s11814-020-0704-1 Export Citation

Deep learning-based initial guess for minimum energy path calculations

Hyunsoo Park, Sangwon Lee, and Jihan Kim^†

Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291, Daehak-ro, Yuseong-gu, Daejeon 34141, Korea

E-mail:

An autoencoder that automatically generates an initial guess for the minimum energy pathway (MEP) calculations has been designed. Specifically, our autoencoder takes in the trajectories of molecular dynamics simulations as its input and facilitates the generation of feasible molecular coordinates. Two molecules (acetonitrile and alanine dipeptide) were tested using the nudged elastic band calculations and the results provided improvements over linear interpolation and image dependent pair potential methods in terms of the number of SCF iterations, demonstrating the utility of using an autoencoder type of an approach for MEP calculations.

Keywords:Deep Learning;Autoencoder;MEP;NEB;Reaction Path

[References]

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[2] Schlegel HB, J. Comput. Chem., 24, 1514 (2003)

[3] Laidler LK. King MC, J. Phys. Chem., 87, 2657 (1983)

[4] Pratt LR, J. Chem. Phys., 85, 5045 (1986)

[5] Elber R, Karplus M, Chem. Phys. Lett., 139, 375 (1987)

[6] Weinan E, Ren W, Vanden-Eijnden E, Phys. Rev. B, 66, 523011 (2002)

[7] Weinan E, Ren W, Vanden-Eijnden E, J. Chem. Phys., 126, 164103 (2017)

[8] Jonsson H, et al., in Classical and quantum dynamics in condensed phase simulations, World Scientific, Singapore (1998).

[9] Sheppard D, Xiao P, Chemelewski W, Johnson DD, Henkelman G, J. Chem. Phys., 136, 074103 (2012)

[10] Henkelman G, Jonsson H, J. Chem. Phys., 113(22), 9978 (2000)

[11] Sheppard D, Trrell R, Henkelman G, J. Chem. Phys., 128, 1 (2008)

[12] Herbol HC, Stevenson J, Clancy P, J. Chem. Theory Comput, 13, 3250 (2017)

[13] Raber LR, Chem. Eng. News, 75, 39 (1997)

[14] Govind N, Petersen M, Fitzgerald G, King-Smith D, Andzelm J, Comput. Mater. Sci., 28, 250 (2003)

[15] Smidstrup S, Pedersen A, Stokbro K, Jonsson H, J. Chem. Phys., 140, 214106 (2014)

[16] Martinez-Nunez E, J. Comput. Chem., 36, 222 (2015)

[17] Wang LP, Titov A, McGibbon R, Liu F, Pande VS, Martinez TJ, Nat. Chem., 6, 1044 (2014)

[18] Wang LP, McGibbon RT, Pande VS, Martinez TJ, J. Chem. Theory Comput., 12, 638 (2016)

[19] Dewyer AL, Arguelles AJ, Zimmerman PM, Wiley Interdiscip. Rev. Comput. Mol. Sci., 8, 1 (2018).

[20] Chen X, Duan Y, Houthooft R, Schulman J, Sutskever I, Abbeel P, Adv. Neural Inf. Process. Syst., 2180 (2016).

[21] Upchurch P, et al., Proc. - 30th IEEE Conf. Comput. Vis. Pattern Recognition, CVPR 2017 2017-Janua, 6090 (2017).

[22] Berthelot D, Goodfellow I, Raffel C, Roy A, 7th Int. Conf. Learn. Represent. ICLR 2019 (2019).

[23] Kramer MA, AIChE J., 37, 233 (1991)

[24] Vincent P, Larochelle H, Lajoie I, Bengio Y, Manzagol PA, J. Mach. Learn. Res., 11, 3371 (2010)

[25] Kingma DP, Welling M, 2nd Int. Conf. Learn. Represent. ICLR 2014 - Conf. Track Proc., 1 (2014).

[26] Plimpton S, J. Comput. Phys., 117, 1 (1997)

[27] Plimpton S, Thomson AP, MRS Bulletin, 37, 513 (2012)

[28] Rappe AK, Casewit CJ, Colwell KS, Goddard WA, Skiff WM, J. Am. Chem. Soc., 114, 10024 (1992)

[29] Kresse G, Hafner J, Phys. Rev. B, 48, 13115 (1993)

[30] Kresse G, Furthmuller J, Hafner J, Phys. Rev. B, 50, 13181 (1994)

[31] Kresse G, Furthmuller J, Phys. Rev. B, 54, 11169 (1996)

[32] Blochl PE, Phys. Rev. B, 50, 17953 (1994)

[33] Perdew JP, Burke K, Ernzerhof M, Phys. Rev. Lett., 77, 3865 (1996)

[34] Bitzek E, Koskinen P, Gahler F, Moseler M, Gumbsch P, Phys. Rev. Lett., 97, 1 (2006)

[35] Henkelman G, Uberuaga BP, Jonsson H, J. Chem. Phys., 113(22), 9901 (2000)

[36] Larsen A, Mortensen JJ, Blomqvist J, Castelli I, Christensen R, Dułak M, Friis J, Groves MN, Hammer B, Hargus C, J. Phys. Condens. Matter, 29, 273002 (2017)

[37] Ren W, Vanden-Eijnden E, Maragakis P, Weinan E, J. Chem. Phys., 123, 134109 (2005)

[38] Allouche A, J. Comput. Chem., 32, 174 (2012)

[39] Bolhuis PG, Dellago C, Chandler D, Proc. Natl. Acad. Sci. U.S.A., 97, 5877 (2000)