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pablo-arantes authored Oct 29, 2024
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Expand Up @@ -37,6 +37,8 @@ The main goal of this work is to demonstrate how to harness the power of cloud-c
12. **Martini+cg2all** [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Martini%2Bcg2all.ipynb) - `Utilizing Vermouth, the Python library that powers Martinize2, to generate the topology and build the simulation box for protein systems using Martini force fields. Additionally, employing cg2at to predict all-atom trajectories from coarse-grained (CG) representations.`
13. **AMBER Mutations** [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Amber_mutations.ipynb) - `Performing mutations on protein/nucleic acid systems and utilizing AMBER to generate the topology and build the simulation box.`

Want to try MD simulation on NAMD using Google Colab? [**Mostafa Sayed**](https://github.com/mabdelmaksoud53) create a colab notebook for running MD simulations using NAMD and CHARMM-GUI inputs. [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/mabdelmaksoud53/Colab_NAMD_Suite/blob/main/MD_NAMD.ipynb)

Tired to "just" run molecular simulations and want to try something new?
**Gabriel Monteiro da Silva** ([@GMondaSilva](https://twitter.com/GMondaSilva)) and I are thrilled to share a colab notebook for running the subsampled AlphaFold2 approach for predicting protein conformational ensembles. Check it out: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GMdSilva/gms_natcomms_1705932980_data/blob/main/AlphaFold2_Traj_v1.ipynb)

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