dcTMD 0.4.1
Analyse targeted molecular dynamics data with dcTMD
License: MIT License
Requires Python: >=3.9
Keywords: enhanced sampling, friction, MD analysis

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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](https://pubs.acs.org/doi/full/10.1021/acs.jctc.8b00835).

> 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](https://pubs.acs.org/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](https://www.moldyn.uni-freiburg.de/publications.html) 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](https://pubs.acs.org/doi/full/10.1021/acs.jctc.8b00835).
- Analysis of separate unbinding pathways as described by [Wolf et al. 2023](https://pubs.aip.org/aip/jcp/article/158/12/124106/2881566/Path-separation-of-dissipation-corrected-targeted).

## Installation
`dcTMD` is available on **PyPI** and **conda-forge**.
#### Install with pip
```bash
pip install dcTMD
```
PyPI project page: [https://pypi.org/project/dcTMD/](https://pypi.org/project/dcTMD/)
#### Install with conda
```bash
conda install conda-forge::dctmd
```
Conda-forge package page:
[https://anaconda.org/conda-forge/dcTMD](https://anaconda.org/conda-forge/dcTMD)
#### Install from GitHub
```bash
python3 -m pip install git+ssh://git@github.com/moldyn/dcTMD.git
```

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