Project ID: plumID:22.031
Name: Rare Event Kinetics from Adaptive Bias Enhanced Sampling
Archive: (browse)
Category: methods
Keywords: OPES Flooding, Kinetics, Rate, OPES, Machine Learning
PLUMED version: 2.9
Contributor: Dhiman Ray
Submitted on: 11 Aug 2022
Publication: D. Ray, N. Ansari, V. Rizzi, M. Invernizzi, M. Parrinello. Rare Event Kinetics from Adaptive Bias Enhanced Sampling.

PLUMED input files

File Compatible with
2D_Potential/s27/plumed.dat tested on master
2D_Potential/s54/plumed.dat tested on master
2D_Potential/s90/plumed.dat tested on master
Ala2/phi/plumed.dat tested on master
Ala2/psi/plumed.dat tested on master
Chignolin/folding/plumed-descriptors.dat tested on master
Chignolin/folding/plumed_rate.dat tested on master
Chignolin/unfolding/plumed-descriptors.dat tested on master
Chignolin/unfolding/plumed_rate.dat tested on master

Last tested: 27 Sep 2022, 18:17:28

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

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