How to install¶

COSMO is a Python package built on OpenMM. It depends on OpenMM plus NumPy, ParmEd, MDAnalysis, mdtraj, and pandas, which are best installed from conda-forge. The steps below target Linux.

Requirements¶

OpenMM >= 7.7 (choose a CUDA toolkit compatible with your NVIDIA driver). getStepCount() is unreliable before 7.7 and is required to restart simulations; OpenMM 8.2 is recommended for better performance.
ParmEd, and the analysis dependencies listed in requirements.txt.

Steps¶

Create and activate a fresh conda/mamba environment with a recent Python (e.g. 3.9+):
```
conda create -n cosmo python=3.10 && conda activate cosmo
```
Install OpenMM 7.7 or later:
```
conda install -c conda-forge openmm=7.7 cudatoolkit=10.2
```
Conda may pick a newer CUDA toolkit by default. Choose a version compatible with your NVIDIA driver.
Install the remaining dependencies. The full list (NumPy, ParmEd, MDAnalysis, mdtraj, pandas, plus analysis-only extras used by scripts/) is in requirements.txt:
```
conda install --file requirements.txt
```
If you use the pip install in step 5, COSMO’s runtime dependencies are pulled in automatically from pyproject.toml; requirements.txt still adds the analysis-only packages.
Download this repository to a target path, for example PATH_TO_CODE/cosmo/.
Install COSMO. There are two main ways.

Two ways to install¶

(I) Add to PYTHONPATH (no install)

Add the repository root to your Python path (persist it in .bashrc):

export PYTHONPATH=$PYTHONPATH:PATH_TO_CODE/cosmo/

This exposes import cosmo and the module form of every tool (python -m cosmo.mdrun, etc.), but not the console commands.

(II) Install with pip

From the repository root (the directory with pyproject.toml). This additionally registers the cosmo-mdrun and other console commands on your CLI:

editable (recommended for development), reflects source edits immediately:
```
pip install -e .
```
regular install, copies the package into site-packages (source edits require a reinstall):
```
pip install .
```

Remember to replace PATH_TO_CODE with your actual path.

Console commands¶

pip install registers these entry points (each also has a module form, python -m <module>):

Command	Module	Purpose
`cosmo-mdrun`	`cosmo.mdrun`	Run an IDP / condensate simulation from an `md.ini`.
`cosmo-csp`	`cosmo.csp.protocol`	Co-translational synthesis on an explicit CG ribosome.
`cosmo-cylinder`	`cosmo.csp.cylinder`	Co-translational synthesis through an analytic tunnel.
`cosmo-csp-movie`	`cosmo.csp.movie`	Stitch per-residue/-stage synthesis trajectories into a VMD movie.
`cosmo-make-mrna`	`cosmo.csp.synth_mrna`	Pre-generate a fastest/slowest synonymous-codon mRNA.

(cosmo-simulation is a back-compat alias for cosmo-mdrun.)

Verify¶

cosmo-mdrun -h     # prints help if the console command is installed
python -c "import cosmo; print(cosmo.__version__)"