Project ID: plumID:23.022
Name: A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar
Archive: https://github.com/luigibonati/mlcolvar/raw/main/docs/notebooks/paper_experiments/paper_experiments.zip
Category: methods
Keywords: collective variables, machine learning, toy model
PLUMED version: 2.9
Contributor: Enrico Trizio
Submitted on: 01 Jun 2023
Publication: L. Bonati, E. Trizio, A. Rizzi, M. Parrinello, A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar. The Journal of Chemical Physics. 159 (2023)

PLUMED input files

File Compatible with
input_data/supervised/state-0/plumed.dat tested on v2.9 tested on master
input_data/supervised/state-1/plumed.dat tested on v2.9 tested on master
input_data/supervised/state-2/plumed.dat tested on v2.9 tested on master
input_data/timelagged/opes-y/plumed.dat tested on v2.9 tested on master
input_data/unsupervised/unbiased/plumed.dat tested on v2.9 tested on master
results/multitask/data/plumed.dat tested on v2.9 tested on master
results/supervised/data/plumed.dat tested on v2.9 tested on master
results/timelagged/deepTICA/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_0/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_1/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_10/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_11/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_12/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_13/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_14/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_15/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_2/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_3/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_4/data/plumed.dat tested on v2.9 tested on master
results/unsupervised/iter_5/data/plumed.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 06:49:26

Project description and instructions
This egg contains the input files to reproduce the simulation biasing different data-driven CVs with the mlcolvar library. We report the study of the movement of a particle in two dimension under the action of a three-states potential obtained by modifying the Muller-Brown potential. The simulations require the ves and pytorch modules of PLUMED and can be run using the ves_md_linearexpansion PLUMED command. In the zip file at the given URL (and in the library documentation, the Jupyter notebooks for training the CVs, running the simulations and analyzing the results can also be found. All the trained CV models are also provided in the zip folder provided at the URL.

Submission history
[v1] 01 Jun 2023: original submission

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