FBM

The code in this repository accompanies the preprint "Force-Guided Bridge Matching for Full-Atom Time-Coarsened Dynamics of Peptides'', by Ziyang yu, Wenbing Huang and Yang Liu.

Dependencies

Our code works well on Linux with CUDA==11.7. It will be required to install pytorch and other dependencies listed below with the corresponding CUDA version (if necessary) on your server.

biopython
mdtraj
openmm
rdkit
torch_scatter
tqdm
e3nn
requests

Alanine Dipeptide (AD) Dataset

The PDB file and coordinates of MD trajectories (.xtc format) of AD can be downloaded from mdshare.

PepMD Dataset

To curate our PepMD dataset, you should first download pdb_seqres.fasta file from PDB. We have provided the script to download and process raw PDB data in data/download.py, please run:

cd data && python download.py --fasta ./pdb_seqres.fasta --save_dir /your/saving/directory

where you should specify a saving directory for PDB and processed peptide files. If all scripts work successfully, there will be summary.jsonl and summary-post.jsonl in your saving directory now.

Then MD simulations can be performed with simulation.py:

python simulation.py --summary /your/saving/directory/summary-post.jsonl --temp 300 --spacing 1000 --gpu 0

where you can specify your own configurations, such as temperature --temp (unit: Kelvin) and frame spacing --spacing (unit: fs). The script will create a directory sim under /your/saving/directory where each peptide has its own sub-directory named by PDB id, including a {PDB-id}_{chain-id}-traj-arrays.npz file containing coordinates, velocities, forces and energies of MD trajectories and a state0.pdb file.

Now we can curate the dataset with train/test splits:

python dataset.py --sim_dir /your/saving/directory/sim --delta 500

where you can specify the coarsened time for prediction --delta (unit: ps). Afterwards there will be train.jsonl and test.jsonl under /your/saving/directory for training and evaluation.

Training

Before running training scripts, first compile TorchMD extensions with:

python setup.py build_ext --inplace

Then you can use the script train.sh for training both FBM-base and FBM with multi GPUs. Note that you should first replace DATA_DIR in the file with /your/saving/directory. You can run the following script to train FBM-base with GPU 0, 1:

GPU=0,1 bash train.sh

For training FBM, please modify the configuration --model_type bbm to --model_type fbm and add another line including --baseline /path/to/FBM-base/checkpoint, where you should replace with the checkpoint file path (.ckpt) of FBM-base.

Evaluation

We have provided different evaluation scripts for various usage.

If you only want to inference trajectories without evaluation, please run:

python inference.py --name {any_name_for_identity} --test_set /path/to/state0.pdb --ckpt /path/to/checkpoint --save_dir /path/to/saving/results --inf_step 1000 --sde_step 30 --guidance 0.05 --gpu 0

where --name is only used to create sub-directory under --save_dir for saving generated trajectories. --test_set is the path to the initial PDB file you are interested in, --ckpt specifies the path to the checkpoint of FBM-base or FBM, --inf_step specifies the trajectory length and --sde_step indicates discrete-time step $T$. If you use the FBM model for inference, it's required to add --guidance to specify the guidance strength.

If you want to evaluate any generated trajectories with MD trajectories, please run:

python evaluate.py --top /path/to/state0.pdb --ref /path/to/MD/trajectories --model /path/to/generated/trajectories

Here --top specifies the .pdb file that describes the topology, --ref and --model specify trajectories generated by MD and the model respectively. We support multiple format for --ref and --model, including: .pdb, .xtc, .npz consisting of the key "positions", .npy.

If you want to inference and evaluate the model on the test set of PepMD (or any other test sets), please run:

python evaluate_all.py --name none --test_set /your/saving/directory/test.jsonl --ckpt /path/to/checkpoint --save_dir /path/to/saving/results --inf_step 1000 --sde_step 30 --guidance 0.05 --gpu 0

License

MIT

Citation

If you find our code useful in your research, please cite the following paper:

@misc{yu2024force,
  title={Force-Guided Bridge Matching for Full-Atom Time-Coarsened Dynamics of Peptides},
  author={Yu, Ziyang and Huang, Wenbing and Liu, Yang},
  year={2024},
  eprint={2408.15126},
  archivePrefix={arXiv},
}