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: 22 Apr 2025, 10:04:23
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.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 30 Jan 2024: original submission
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