"Targeting the intrinsically disordered AR-NTD through a machine learn-ing-based enhanced sampling workflow"
The training of the models was based on the mlcolvar library.
The REST3 tutorial is available here: https://github.com/mdlab-um/REST3_tutorial.
The SWISH tutorial is available here: https://github.com/Gervasiolab/Gervasio-Protein-Dynamics/tree/master/swish_bootcamp.
All molecular dynamics simulations were conducted using GROMACS 2022.6, integrated with the PLUMED 2.9.0 plugin and the PyTorch 2.2.1 library.
The contents of the repository are organized as follows:
- 0-7: input files for REST simulations
- setup: script for scaling the top Hamiltonian
- mlcv: frozen torchscript models for AE CV
- 1-9: input files for SWISH simulations
- 1-9: input files for Binding FES simulations
- 1-9/states Structural files of the free-energy minima conformations