Project ID: plumID:23.032
Name: Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics
Archive: https://zenodo.org/record/8246298/files/ptltsne_nest.zip
Category: bio
Keywords: metadynamics, tSNE, neural network, machine learning, trp-cage, folding
PLUMED version: 2.9
Contributor: Vojtech Spiwok
Submitted on: 14 Aug 2023
Publication: H. Hradiská, M. Kurečka, J. Beránek, G. Tedeschi, V. Višňovský, A. Křenek, V. Spiwok, Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics. The Journal of Physical Chemistry B. 128, 903–913 (2024)

PLUMED input files

File Compatible with
mtd1/plumed.dat tested on v2.9 tested on master
mtd2/plumed.dat tested on v2.9 tested on master
pt/plumedpt.dat tested on v2.9 tested on master
ptmtd/plumedpt.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 06:47:30

Project description and instructions
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 using Gromacs (2021.4, 2021), Plumed (2.8.0, 2.9.0) and other codes available here and here.

Submission history
[v1] 14 Aug 2023: original submission

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plumeDnest:23.032