MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, Amber or DL_POLY; it also reads other formats (e.g. PDB files and XYZ format trajectories; see the supported coordinate formats for the full list). It can write most of these formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol.

Researchers should cite this work as follows:

• (2024), "MDAnalysis," https://sciencegateways.org/resources/mdanalysis.

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1. MDAnalysis
2. Molecular Dynamics
3. PDB format
4. softwareEntry