46 lines
1.6 KiB
Markdown
46 lines
1.6 KiB
Markdown
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# mdevaluate
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Mdevaluate is a Python package to perform analyses of Molecular Dynamics simulations.
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An online documentation is available at [mdevaluate.github.io](https://mdevaluate.github.io).
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Mdevaluate provides a flexible interface for the detailed analysis of dynamical and statical properties of molecular systems.
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It's main focus is the analysis of Gromacs data, but with the help of external packages ([MDAnalysis](https://www.mdanalysis.org/))
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it can also handle file formats, used by other simulation software.
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```python
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import mdevaluate as md
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# load the simulation
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tr = md.open(
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directory='/path/to/simulation',
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topology='topol.tpr',
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trajectory='traj.xtc'
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)
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# select a subset of atoms
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water_oxygen = tr.subset(residue_name='SOL', atom_name='OW')
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# calculate the mean squared displacement for this subset
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time, msd = md.correlation.shifted_correlation(
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md.correlation.msd, water_oxygen, average=True
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)
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```
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## Installation
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The package requires the Python package [pygmx](https://github.com/mdevaluate/pygmx),
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which handles reading of Gromacs file formats.
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Installation of pygmx is described in its own repository.
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The mdevaluate package itself is plain Python code and, hence, can be imported from its directory directly,
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or may be installed via setuptools to the local Python environment by running
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python setup.py install
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## Running the tests
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Mdevaluate includes a test suite that can be used to check if the installation was succesful.
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It is based on `py.test` and located in the test directory of this repository.
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Make sure py.test is installed and run `py.test` within the repository to check if all tests pass.
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