Calculation of Euclidean distances between periodic images
Description
Python code to calculate euclidean distances between periodic images in a (molecular dynamics)
simulation trajectory. Returns the minimum distance between periodic images, which is useful to
determine if the simulation box is too small and the periodic images 'see' each other. Functionality
equivalent to g_mindist of the GROMACS suite (url).
Requirements
-
Python libraries:
- cython
- numpy
- mdtraj
- OpenMM (for mmCIF support)
-
Other:
- OpenMP (for parallelizable version)
Installation / Usage
git clone https://github.com/JoaoRodrigues/pbc_mindist
cd pbc_mindist
conda env create -n pbc_mindist -f environment.yml
source activate pbc_mindist
python setup.py install
pbc_mindist yourtrajectory.dcd yourtopology.pdb --backbone
Caveats
- Reimaging function will fail with
--alpha_carbons. Reimage trajectory first and save the coordinates/topology separately. - Not tested on Windows/OSX
- Compilation will fail without OpenMP (setup.py could use fixing...)
License
Code is licensed under the open-source Apache License (version 2.0).
See LICENSE for more details, but essentially, if you use it, just give
credit and if you publish something with it, just add the URL of this
repository in your Methods section.