Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics

• DOI: 10.1021/acs.jpcb.3c05669
• Publication Date: 2024-01-18T19:46:14Z
• Authors: Helena Hradiská; Martin Kurečka; Jan Beránek; Guglielmo Tedeschi; Vladimír Višňovský; Aleš Křenek; Vojtěch Spiwok
• Keywords: 0303 health sciences; 03 medical and health sciences

Supporting information for: Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics by H. Hradiská, M. Kurečka, J. Beránek, G. Tedeschi, V. Višňovský, A. Křenek, V. Spiwok Supplementary files for the analysis by Plumed Nest (https://www.plumed-nest.org/). Data for metadynamics with two parametric time-lagged tSNE collective variables are in the mtd1 directory. Data for metadynamics with two parametric time-lagged tSNE collective variables and alphaRMSD are in the mtd2 directory. Data for parallel tempering metadynamics with two parametric time-lagged tSNE collective variables are in the ptmtd directory. Data for reference parallel tempering simulations are in the pt directory. The results were obtained by Gromacs (2021.4, 2021), Plumed (2.8.0, 2.9.0) and other codes: https://github.com/spiwokv/ptltsne https://github.com/kurecka/plumed2/tree/uvt_extensions