Project ID: plumID:24.019
Name: Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning
Archive: https://zenodo.org/records/13343727/files/ALICE_ala2_ala10.zip
Category: bio
Keywords: OPES, machine learning, protein folding, adaptive sampling
PLUMED version: 2.9
Contributor: Mingyuan Zhang
Submitted on: 19 Aug 2024
Last revised: 03 Oct 2024
Publication: M. Zhang, H. Wu, Y. Wang, Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning. Journal of Chemical Theory and Computation. 20, 8569–8582 (2024)
PLUMED input files
Last tested: 22 Apr 2025, 09:57:28
Project description and instructions
features.dat are the PLUMED driver files of input features for machine learning adaptive sampling trajectories. ref.dat are the PLUMED driver files of reference CV for adaptive sampling trajectories. plumed.dat are the actual OPES simulation files for enhanced sampling. For details, we refer the users to the original paper or this following Github link. Softwares: Gromacs 2023 patched with PLUMED 2.9.0.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 19 Aug 2024: original submission
[v2] 03 Oct 2024: updated info
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