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Acellera
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AceFF-2.0

Graph Machine Learning
torchmd-net
chemistry
molecular simulations
machine learning potentials
neural network potentials
drug discovery
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update example links

#4
by sfarracellera - opened
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  1. README.md +6 -4
README.md CHANGED
@@ -50,6 +50,8 @@ The table shows the results on the [Wiggle150](https://pubs.acs.org/doi/10.1021/
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  *Performance of MLIPs on Wiggle150 benchmark*
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  ---
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  ## Key Features
@@ -65,10 +67,10 @@ The table shows the results on the [Wiggle150](https://pubs.acs.org/doi/10.1021/
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  ## Usage
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  1. [Example notebooks](https://github.com/Acellera/aceff_examples) are available in **Google Colab**, demonstrating the use of Acellera AceFF with OpenMM and ASE.
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- - Single point calculation with ASE [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Acellera/aceff_examples/blob/main/notebooks/aceff_single_point_calculation.ipynb)
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- - ML molecular dynamics of a small molecule with OpenMM [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Acellera/aceff_examples/blob/main/notebooks/aceff_MD_example.ipynb)
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- - MM/ML protein-ligand simulations with OpenMM [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Acellera/aceff_examples/blob/main/notebooks/aceff_protein_ligand.ipynb)
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  2. Run ML potential molecular simulations of a small molecule using ACEMD with this [tutorial](https://software.acellera.com/acemd/nnp.html), e.g., to minimize.
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  3. For a tutorial on running mixed protein-ligand simulations, refer to [NNP/MM in ACEMD](https://software.acellera.com/acemd/nnpmm.html).
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  *Performance of MLIPs on Wiggle150 benchmark*
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+ Many more benchmarks are reported in the [paper](https://arxiv.org/abs/2601.00581), including torsion scans and speed.
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  ---
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  ## Key Features
 
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  ## Usage
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  1. [Example notebooks](https://github.com/Acellera/aceff_examples) are available in **Google Colab**, demonstrating the use of Acellera AceFF with OpenMM and ASE.
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+ - Single point energy calculator with ASE. [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Acellera/aceff_examples/blob/main/notebooks/aceff_single_point_calculation.ipynb)
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+ - Batch minimization and molecular dynamics with PyTorch. [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Acellera/aceff_examples/blob/main/notebooks/aceff_batched_minimization_and_md.ipynb)
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+ - Running MD for a small molecule in vacuum with OpenMM. [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Acellera/aceff_examples/blob/main/notebooks/aceff_openmm_md_example.ipynb)
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+ - Running MD for a protein ligand complex using MM/ML mechanical embedding scheme with OpenMM. [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Acellera/aceff_examples/blob/main/notebooks/aceff_openmm_protein_ligand.ipynb)
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  2. Run ML potential molecular simulations of a small molecule using ACEMD with this [tutorial](https://software.acellera.com/acemd/nnp.html), e.g., to minimize.
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  3. For a tutorial on running mixed protein-ligand simulations, refer to [NNP/MM in ACEMD](https://software.acellera.com/acemd/nnpmm.html).
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