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https://github.com/giorginolab/2024-molsim-unipd

Material for the Molecular Simulations module (Prof. Fuxreiter)

https://github.com/giorginolab/2024-molsim-unipd

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (7.3%) to scientific vocabulary
Last synced: 5 months ago · JSON representation

Repository

Material for the Molecular Simulations module (Prof. Fuxreiter)

Basic Info
  • Host: GitHub
  • Owner: giorginolab
  • License: gpl-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 30 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License

README.md

2024-MolSim-UniPD

Material for the Molecular Simulations module (for Prof. Fuxreiter)

Toni Giorgino

How to run

The code contained in this repo is structure in large part as IPython notebooks. They can be run in three ways:

  • On your local machine. That's probably the easiest and most didactic for interpreting the intermediate files.
  • On Google Colab. Just open Colab and point it to the file's URL. Simulations run much faster if you request a GPU runtime.
  • On Binder. Somewhat slow but comes with a pre-installed environment. Open in binder

Day 2

Here are the links:

  • Analysis with MDTraj: https://github.com/giorginolab/MD-Tutorial-Data/blob/main/notebooks/2MDTrajanalysis.ipynb . If "open in Colab" does not work automatically, manually open Colab and point it to said address.
  • Docking: https://github.com/giorginolab/2024-MolSim-UniPD/blob/main/docking/Docking_2024.ipynb or here . Same as above.

Remember that we use condacolab, so there will be an initial restart of the kernel.

Owner

  • Name: Giorgino Laboratory
  • Login: giorginolab
  • Kind: organization
  • Location: Milan, Italy

Computational Biophysics

GitHub Events

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