Project ID: plumID:23.030
Name: Data Driven Classification of Ligand Unbinding Pathways
Archive: https://github.com/dhimanray/DTW_Path_Classification/archive/main.zip (browse)
Category: bio
Keywords: OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time
PLUMED version: 2.9
Contributor: Dhiman Ray
Submitted on: 04 Aug 2023
Last revised: 28 Feb 2024
Publication: D. Ray, M. Parrinello, Data-driven classification of ligand unbinding pathways. Proceedings of the National Academy of Sciences. 121 (2024)

PLUMED input files

File Compatible with
T4L_benzene/opes_explore/template/plumed.dat tested on v2.10 tested on master
…zene/opes_explore/template/plumed_contact_6_12.dat tested on v2.10 tested on master
…L_benzene/opes_flooding/template_barr30/plumed.dat tested on v2.10 tested on master
…s_flooding/template_barr30/plumed_contact_6_12.dat tested on v2.10 tested on master
ala2/template/plumed.dat tested on v2.10 tested on master
mueller/template/plumed.dat tested on v2.10 tested on master

Last tested: 22 Apr 2025, 10:03:19

Project description and instructions
Simulations of Alanine Dipeptide and Benzene-T4-Lysozyme complex are conducted using GROMACS v2021.5. The objectives of these simulations are to explore reactive pathways and to classify the transition paths using Dynamic Time Warping.

Click here to open manual pages for actions used in this project.

Submission history
[v1] 04 Aug 2023: original submission
[v2] 28 Feb 2024: updated doi

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plumeDnest:23.030