Installation

HTMD is published on PyPI as acellera-htmd and also available as a conda package. Pip is the default; use conda if you need the bundled external tools (CHARMM build helpers, etc.) that conda packages but pip does not.

With pip (default)

python -m venv .venv
source .venv/bin/activate
pip install acellera-htmd

With conda

We recommend Miniforge: conda-forge/miniforge. Once it’s installed:

conda create -n htmd
conda activate htmd
conda install htmd -c acellera -c conda-forge

Some HTMD features (e.g. CHARMM building, ACEMD integration) depend on tools that conda can install but pip cannot. If you hit a FileNotFoundError for an external binary, switch to the conda install.

Licence registration

HTMD prints a short copyright reminder on import in interactive sessions. To silence it and let Acellera know who is using HTMD, you can register your install once:

htmd_register

Registration is optional - the package works fully without it.

Verify

from htmd.ui import *

mol = Molecule("3PTB")
print(mol.numAtoms)

Expected output: an integer count of atoms in PDB entry 3PTB.

For contributors: uv

If you’re developing HTMD (running the test suite, building docs, working from a checkout), use uv:

uv sync --group dev      # install dev + test deps
uv sync --group docs     # add the doc-build deps
uv run pytest            # run the test suite
cd doc && uv run make html

See the pyproject.toml [dependency-groups] table for the full list of optional dependency groups.