mcwitt/timemachine-demo

Jupyter Notebook

Timemachine Demo

Notebook introducing the timemachine molecular dynamics engine with simple examples of vacuum Langevin dynamics and free energy calculations.

Quick start

An OpenEye license is currently required. Specify the path to the license file, e.g. by setting OE_DIR:
```
export OE_DIR=~/.openeye
```

Using conda/mamba

To enable CUDA support (requires Linux and a compatible GPU), install CUDA Toolkit 11.6 or greater. Otherwise, set
```
export SKIP_CUSTOM_OPS=1
```
to skip building CUDA kernels.

Install and activate environment with conda (or mamba)

conda env create -f environment.yml -n timemachine-demo
conda activate timemachine-demo

Launch Jupyter Lab
```
jupyter lab
```

Using Nix (Linux+CUDA only)

Install the Nix package manager and enable flakes support.
To enter a reproducible Jupyter Lab environment with all the required dependencies
```
nix run
```
To enter a development environment
```
nix develop
```