Project ID: plumID:22.017
Name: Water regulates the residence time of Benzamidine in Trypsin
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 tested on v2.9 tested on master
RATE/plumed.dat tested on v2.9 tested on master

Last tested: 23 May 2024, 16:14:35

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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