https://github.com/zincware/znmdakit

https://github.com/zincware/znmdakit

Last synced: 10 months ago
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• Host: GitHub
• URL: https://github.com/zincware/znmdakit
• Owner: zincware
• License: apache-2.0
• Created: 2024-02-23T09:23:16.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2025-06-02T19:34:54.000Z (12 months ago)
• Last Synced: 2025-06-03T10:47:56.329Z (12 months ago)
• Language: Python
• Size: 709 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 9
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
[![ZnTrack](https://img.shields.io/badge/Powered%20by-ZnTrack-%23007CB0)](https://zntrack.readthedocs.io/en/latest/)

[![zincware](https://img.shields.io/badge/Powered%20by-zincware-darkcyan)](https://github.com/zincware)

# ZnMDAKit

[ZnTrack](https://github.com/zincware/ZnTrack) enabled [MDAnalysis Toolkits](https://mdakits.mdanalysis.org/) with full parameter and result tracking capabilities.

## Example

```python

import znmdakit

project = znmdakit.Project()

with project:

    system = ips.Smiles2Gromacs(

        smiles=[BMIM, BF4],

        density=0.5,

        count=[64, 64],

        labels=["Im", "BF"],

        config_files=mdp_files,

        fudgeLJ=1,

        fudgeQQ=1,

        itp_files=itps,

        pdb_files=pdbs,

        tolerance=1.8,

        cleanup=True,

        maxwarn=0,

    )

    universe = znmdakit.Universe(

        # data_file=znflow.resolve(system.traj_file), # hotfix for https://github.com/zincware/ZnTrack/pull/875

        data=system.frames, # can be either one

        residues={"BF": BF4, "Im": BMIM},

    )

with project.group("BF4"):

    znmdakit.InterRDF(

        universe=universe.universe,

        g1="name COM and resname BF", # replace with e.g. name O and set apply_com_transform=False

        g2="name COM and resname BF",

        nbins=1000,

        apply_com_transform=True,

    )

    msd = znmdakit.EinsteinMSD(

        universe=universe.universe,

        select="name COM and resname BF",

        timestep=0.001, # ps

        sampling_rate=1000, # ps

        apply_com_transform=True,

    )

    znmdakit.SelfDiffusionFromMSD(

        data=msd,

        start_time=2000,

        end_time=7000,

        always_changed=False,

    )

project.build()

```

## Available Nodes

- `znmdakit.RDF`

- `znmdakit.EinsteinMSD`