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, A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations (2024)

PLUMED input files

File Compatible with
amylase/opes_flooding_qmmm/plumed.dat tested on v2.9 tested on master
chorismate_mutase/opes_flooding_qmmm/plumed.dat tested on v2.9 tested on master
chorismate_mutase/opes_mm/plumed.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 06:46:19

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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