A python molecular dynamics data analysis tool.
- python3: >=3.8
Fishmol is still under development, but you can install it locally:
- Download the code from GitHub:
git clone https://github.com/Lei-Lei-alpha/fishmol.git- Change to the fishmol directory:
cd fishmol- Install fishmol
pip install -e ./- Run the following command in your terminal to see if fishmol is successfully installed:
fishmol Welcome! ▄▄█▀ FishMol
▄▄███▀ version 0.0.1
○ ▄▄█████▀ ○
○ ▄▄████████▄ /
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○ ▄▄▄████████████████████▄▄ \
▄▄▄██████▀███████████████████████▄▄ ○--○ ▄
▄▄████████████ ██████████████████████████▄▄ / ▄▄█▀
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▀▀▄ Contact: [email protected]
Please refer to docs for usage.
- I/O of trajectory files in
xyzformat- calibration of the trajectory file by fixing the centre of mass
- Simple view function
- Simple manipulate of trajectory: filter, select etc
- Calculation of mean square displacement (MSD) and diffusion coefficient
- the anisotropy of diffusion by calculating the projection of MSD and diffusion coefficient along specified directions
- hydrogen bond recognition and lifetime analysis
- the reorientation lifetime of vectors
- the distribution function of a range of scalars (including the radial distribution function, angular distribution function, dihedral angle distribution function)
- 2D combined distribution functions
- Van Hove correlation function
- dimer lifetime correlation function
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