Project ID: plumID:22.031
Name: Rare Event Kinetics from Adaptive Bias Enhanced Sampling
Archive: https://github.com/dhimanray/OPES-Flooding/archive/main.zip (browse)
Category: methods
Keywords: OPES Flooding, Kinetics, Rate, OPES, Machine Learning
PLUMED version: 2.9
Contributor: Dhiman Ray
Submitted on: 11 Aug 2022
Last revised: 14 Nov 2022
Publication: D. Ray, N. Ansari, V. Rizzi, M. Invernizzi, M. Parrinello, Rare Event Kinetics from Adaptive Bias Enhanced Sampling. Journal of Chemical Theory and Computation. 18, 6500–6509 (2022)
PLUMED input files
Last tested: 17 Apr 2024, 07:17:27
Project description and instructions
Introducing the OPES Flooding method for calculating kinetics of rare event processes. It is tested on model systems and folding/unfolding of chignolin. The MD engine used is GROMACS 2021. The Deep-LDA and Deep-TICA CV were trained using Pytorch 1.8.2 and mlcvs package. Note. The OPES flooding method is available from PLUMED version 2.8. But the Deep-LDA and Deep-TICA CV we used in this work are implemented in PLUMED 2.9.
Submission history
[v1] 11 Aug 2022: original submission
[v2] 14 Nov 2022: updated doi
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