Project ID: plumID:22.017
Name: Water regulates the residence time of Benzamidine in Trypsin
Archive: https://github.com/narjesansari/LigandBinding_Trypsin_FES_RATE/archive/refs/heads/main.zip
Category: bio
Keywords: ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA
PLUMED version: 2.8
Contributor: Narjes Ansari
Submitted on: 11 Apr 2022
Publication: N. Ansari, V. Rizzi, M. Parrinello, Water regulates the residence time of Benzamidine in Trypsin. Nature Communications. 13 (2022)
PLUMED input files
| File | Compatible with |
|---|---|
| FES/plumed.dat |   |
| RATE/plumed.dat | |
Last tested: 11 Sep 2024, 14:30:34
Project description and instructions
This egg contains the input files for replicating Trypsin-Benzamidine ligand binding simulations with Deep-LDA and Deep-TICA CVs. These CVs accelerate water throughout the binding/unbinding events. For more information about Deep-LDA, we refer to plumID:20.004 and about Deep-TICA to plumID:21.039. The CVs were trained with Pytorch version 1.4 and the simulations were run with Gromacs 2020.4.
Submission history
[v1] 11 Apr 2022: original submission
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