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dcTMD

This package aids in the analysis of dissipation-corrected targeted molecular dynamics (dcTMD) simulations. The method enforces rare unbinding events of ligands from proteins via a constraint pulling bias. Subsequently, free energy profiles and friction factors are estimated along the unbinding coordinate. For a methodological overview, see our article.

S. Wolf, and G. Stock,
Targeted molecular dynamics calculations of free energy profiles using a nonequilibrium friction correction.,
J. Chem. Theory Comput. 2018 14 (12), 6175-6182,
doi: 10.1021/acs.jctc.8b00835

This package will be published soon:

M. Jäger, V. Tänzel, D. Nagel, and S. Wolf,
Dissipation Corrected Targeted Molecular Dynamics,
in preparation 2025

We kindly ask you to cite these articles in case you use this software package for published works.

Features

• Intuitive usage via module and CI
• Sklearn-style API for fast integration into your Python workflow
• Supports Python 3.9-3.14
• Multitude of publications with dcTMD

Implemented Key Functionalities

• Estimation of free energy profiles and friction factors along the unbinding coordinate of ligands as described by Wolf and Stock 2018.
• Analysis of separate unbinding pathways as described by Wolf et al. 2023.

Installation

dcTMD is available on PyPI and conda-forge.

From PyPI

pip install dcTMD

PyPI project page: https://pypi.org/project/dcTMD/

From conda-forge

conda install conda-forge::dctmd

Conda-forge package page: https://anaconda.org/conda-forge/dcTMD

From GitHub

python3 -m pip install git+ssh://git@github.com/moldyn/dcTMD.git

Local development environment

The runtime dependencies are listed in requirements.txt and environment.yml. For a local checkout, install them with:

python3 -m pip install -r requirements.txt

For conda users, create the environment with:

conda env create -f environment.yml
conda activate dcTMD

Usage

Check out the documentation for an overview over all modules as well as the tutorials.