Update README.md

README.md

@@ -1,5 +1,82 @@
----
-license: other
-license_name: asl
-license_link: LICENSE
----
+---
+license: other
+license_name: asl
+license_link: LICENSE
+tags:
+- chemistry
+---
+# FeNNix-Bio1
+
+An efficient machine-learning interatomic potential for molecular dynamics simulations of organic and biological systems trained on an extension of the SPICE2 dataset.
+The model comes in two sizes (S and M).
+
+## Model Details
+
+- **Developed by:** T. Plé, O. Adjoua, A. Benali, E. Posenitskiy, C. Villot, L. Lagardère and J.-P. Piquemal
+- **License:** Acadamic Software License (ASL)
+
+- **Repository:** [github.com/FeNNol-tools/FeNNol-PMC/tree/main/FENNIX-BIO1](https://github.com/FeNNol-tools/FeNNol-PMC/tree/main/FENNIX-BIO1)
+- **Paper:** [DOI:10.26434/chemrxiv-2025-f1hgn-v4](https://chemrxiv.org/engage/chemrxiv/article-details/69399703bc44e47cf4980c4e)
+- **Code:** [github.com/FeNNol-tools/FeNNol](https://github.com/FeNNol-tools/FeNNol)
+
+## Uses
+
+- Molecular dynamics simulations of organic and biological systems
+- Geometry optimization
+- Scoring (Binding free energy calculations)
+
+## How to Get Started with the Model
+
+Download one of the models from [github.com/FeNNol-tools/FeNNol-PMC/tree/main/FENNIX-BIO1](https://github.com/FeNNol-tools/FeNNol-PMC/tree/main/FENNIX-BIO1).
+Install the [FeNNol](https://github.com/FeNNol-tools/FeNNol) library
+```bash
+pip install fennol[cuda]
+```
+The model can easily be used with ASE:
+```python
+from fennol.ase import FENNIXCalculator
+import sys
+from ase import Atoms
+from ase.md.verlet import VelocityVerlet
+from ase.io import read
+from ase import units
+import time
+
+xyz_file = sys.argv[1]
+atoms = read(xyz_file)
+calc = FENNIXCalculator(model="fennix-bio1M.fnx", gpu_preprocessing=True)
+atoms.calc = calc
+
+dyn = VelocityVerlet(atoms, 1.0 * units.fs)  # 1 fs time step
+nsteps = 100_000
+steps_per_print = 100
+t0 = time.time()
+for step in range(1,nsteps+1):
+    dyn.run(1)
+    if step % steps_per_print == 0:
+        t1 = time.time()
+        steps_per_second = steps_per_print / (t1 - t0)
+        print(f"Step: {step:10}, Energy: {atoms.get_potential_energy():15.5f} eV, Steps/s: {steps_per_second:.2f}")
+        t0 = time.time()
+```
+
+For better performance, we recommend directly using FeNNol's MD engine
+(see the [example](https://github.com/FeNNol-tools/FeNNol/tree/main/examples/md) directory in FeNNol's github repo)
+
+
+## Citation 
+
+Plé T, Adjoua O, Benali A, Posenitskiy E, Villot C, Lagardère L, et al. A Foundation Model for Accurate Atomistic Simulations in Drug Design.
+ChemRxiv. 2025; doi:10.26434/chemrxiv-2025-f1hgn-v4 
+
+**BibTeX:**
+
+```
+@article{Ple-2025,
+  title={A Foundation Model for Accurate Atomistic Simulations in Drug Design},
+  DOI={10.26434/chemrxiv-2025-f1hgn-v4},
+  journal={ChemRxiv},
+  author={Plé, Thomas and Adjoua, Olivier and Benali, Anouar and Posenitskiy, Evgeny and Villot, Corentin and Lagardère, Louis and Piquemal, Jean-Philip},
+  year={2025}
+}
+```