/goat

GOAl conditioned Transition path sampling (TPS)

Primary LanguageJupyter Notebook

Collective Variable Free Transition Path Sampling with Generative Flow Networks

Environment settings

This code runs on version python version: 3.9

Install the followings:

  • Openmmtools for Molecular Dynamics (MD) simulation 
    conda install -c conda-forge openmmtools
  • Openmmforcefields for forcefields of large proteins 
    git clone https://github.com/openmm/openmmforcefields.git
  • Other packages 
    pip install torch tqdm wandb mdtraj matplotlib

Usage

  • Training: Run the following command to start training:

    bash scripts/train_alanine.sh

  • Evaluation: Run the following command to perform evaluation:

    bash scripts/eval_alanine.sh

Reproduce

  • Table: Run the following command to reproduce the table: 
    bash scripts/reproduce_table.sh