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: 16 Jan 2025, 20:18:10

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.

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

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plumeDnest:23.030