nmrformd
NMRforMD is a python script for the calculation of NMR relaxation time T1 and T2 from molecular dynamics trajectory file.
Science Score: 46.0%
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1 of 2 committers (50.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (16.5%) to scientific vocabulary
Keywords
Repository
NMRforMD is a python script for the calculation of NMR relaxation time T1 and T2 from molecular dynamics trajectory file.
Basic Info
- Host: GitHub
- Owner: simongravelle
- License: gpl-3.0
- Language: Python
- Default Branch: main
- Homepage: https://nmrformd.readthedocs.io/
- Size: 309 MB
Statistics
- Stars: 26
- Watchers: 2
- Forks: 5
- Open Issues: 0
- Releases: 11
Topics
Metadata Files
README.md
NMRforMD
Dipolar Nuclear Magnetic Resonance for Molecular Dynamics (NMRforMD) simulations is a Python toolkit designed for the computation of dipolar NMR relaxation times (the so called $T1$ and $T2$) from molecular dynamics simulations. Used in combination with MDAnalysis, NMRforMD allows for the analysis of trajectory files from any MDAnalysis-compatible simulation package, including LAMMPS and GROMACS.
Migration
This repository will progressively be migrated on here, and the most up-to-date page will be https://nmrdfrommd.github.io.
Documentation
Details about installation and use of NMRforMD are given in the documentation. The documentation also contains a description of the theory behind dipolar dipolar NMR calculations, as well as details on some common pitfalls of NMR calculations.
Figure: Examples of systems that can be analyzed using NMRforMD, from left to right: a bulk water system, a lennard-jones fluid, and a lysozyme in water.
Datasets
Two molecular dynamics datasets are available on Github. One is a polymer in water system generated using LAMMPS, the second is a water confined in silica generated using GROMACS. Both datasets are required to follow the tutorials provided in the documentation.
Warning
The code has mostly been tested in the case of 1H-NMR (i.e. spin 1/2). It is also important to keep in mind that NMRforMD only works for dipolar interaction, not quadrupolar interaction.
Known issues
For very large trajectory file, the code requires a lot of memory. The code is not adapted to triclinic box, convert your trajectory to orthorhombic prior to calculation. This code is still in development, please raise an issue here if you encounter another problem.
For developers
If you intend to make modification to the code, please raise an issue or send me an email first. Then, fork the repository, apply your changes, then make a pull request that will be reviewed.
Clone the repository with its submodules as follow:
bash
git clone https://github.com/simongravelle/nmrformd.git --recurse-submodule
Find more instructions here.
Acknowledgments
This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skodowska-Curie grant agreement No 101065060.
Owner
- Name: Simon Gravelle
- Login: simongravelle
- Kind: user
- Location: Grenoble
- Company: LIPhy
- Website: https://simongravelle.github.io/
- Twitter: GravelleSimon
- Repositories: 12
- Profile: https://github.com/simongravelle
MSCA research fellow
GitHub Events
Total
- Watch event: 6
- Push event: 3
- Fork event: 1
Last Year
- Watch event: 6
- Push event: 3
- Fork event: 1
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 235
- Total Committers: 2
- Avg Commits per committer: 117.5
- Development Distribution Score (DDS): 0.187
Top Committers
| Name | Commits | |
|---|---|---|
| Simon Gravelle | s****e@l****r | 191 |
| Simon Gravelle | s****e@i****e | 44 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 1
- Total pull requests: 2
- Average time to close issues: 1 day
- Average time to close pull requests: 17 minutes
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- simongravelle (1)
Pull Request Authors
- simongravelle (2)
Top Labels
Issue Labels
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Packages
- Total packages: 1
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Total downloads:
- pypi 40 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 9
- Total maintainers: 1
pypi.org: nmrformd
Calculate dipolar NMR relaxation time from molecular dynamics trajectory file
- Homepage: https://github.com/simongravelle/nmrformd
- Documentation: https://nmrformd.readthedocs.io/
- License: GNU GENERAL PUBLIC LICENSE
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Latest release: 0.1.1
published over 2 years ago
Rankings
Maintainers (1)
Dependencies
- furo *
- scipy *
- sphinx *
- coverage *
- flake8 *
- pytest *
- mdanalysis *
- numpy *
- pytest *
- scipy *
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