Mdevaluate is a Python package to perform analyses of Molecular Dynamics simulations. An online documentation is available at mdevaluate.github.io. Mdevaluate provides a flexible interface for the detailed analysis of dynamical and statical properties of molecular systems. It's main focus is the analysis of Gromacs data, but with the help of external packages (MDAnalysis) it can also handle file formats, used by other simulation software.

import mdevaluate as md

# load the simulation
tr = md.open(
	directory='/path/to/simulation',
	topology='topol.tpr',
	trajectory='traj.xtc'
)
# select a subset of atoms
water_oxygen = tr.subset(residue_name='SOL', atom_name='OW')

# calculate the mean squared displacement for this subset
time, msd = md.correlation.shifted_correlation(
	md.correlation.msd, water_oxygen, average=True
)

Installation

The mdevaluate package itself is plain Python code and, hence, can be imported from its directory directly, or may be installed via setuptools to the local Python environment by running

python setup.py install

When you are using uv you can install it with:

uv venv some_folder
source some_folder/bin/activate
uv pip install https://gitea.pkm.physik.tu-darmstadt.de/IPKM/mdevaluate.git

Running the tests

Mdevaluate includes a test suite that can be used to check if the installation was succesful. It is based on py.test and located in the test directory of this repository. Make sure py.test is installed and run py.test within the repository to check if all tests pass.