mdciao

https://www.mdciao.org

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mdciao is a Python module for accessible analysis and visualization of molecular dynamics simulation...

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### Run Built-in Command-Line Examples

Source: https://www.mdciao.org

Execute this command to access a list of all built-in command-line toy-examples provided by mdciao. This is useful for quickly testing or demonstrating the module's capabilities.

```bash
mdc_examples.py

```

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### Access Live Jupyter Notebooks

Source: https://www.mdciao.org

Run this command to open live Jupyter notebooks for interactive exploration of mdciao's features. These notebooks showcase real-life, elaborated examples and are part of the Jupyter Notebook Gallery.

```bash
mdc_notebooks.py

```

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### Calculate Residue-Residue Distances and Contacts

Source: https://www.mdciao.org

Use this command-line tool to calculate time-traces of residue-residue distances, contact frequencies, and distance distributions from MD simulation files. Specify topology, trajectory, and target residues. The output includes generated files for visualization and data analysis.

```bash
mdc_neighborhoods.py top.pdb traj.xtc --residues L394

```

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