Project ID: plumID:24.001
Name: A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations
Archive: https://github.com/dhimanray/Enzyme_Kinetics_OPES_flooding/archive/main.zip (browse)
Category: bio
Keywords: OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis
PLUMED version: 2.9
Contributor: Dhiman Ray
Submitted on: 30 Jan 2024
Publication: D. Ray, S. Das, U. Raucci, Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations. Journal of Chemical Information and Modeling. 64, 3953–3958 (2024)
PLUMED input files
| File | Compatible with |
|---|---|
| amylase/opes_flooding_qmmm/plumed.dat |   |
| chorismate_mutase/opes_flooding_qmmm/plumed.dat | |
| chorismate_mutase/opes_mm/plumed.dat | |
Last tested: 23 Apr 2025, 10:18:01
Project description and instructions
To perform OPES simulation at MM level we used GROMACS v2022. For OPES flooding simulation at QM/MM level we used CP2K v9.1. Python scripts have been used for rescaling transition times and for KS tests.
Submission history
[v1] 30 Jan 2024: original submission
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