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Published August 14, 2023 | Version v1
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Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics

Authors/Creators

  • 1. Helena
  • 2. Martin
  • 3. Jan
  • 4. Guglielmo
  • 5. Vladimír
  • 6. Aleš
  • 7. Vojtěch

Description

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

 

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