MDAnalysis
Program to analyze trajectories from molecular dynamics simulations. It supports many file formats (CHARMM, DL_POLY, GROMACS, LAMMPS, NAMD, Amber) and allows for distance calculations, RMSD, and complex analysis.
Features
- Formats: DCD, XTC, TRR, NetCDF, PDB
- Analysis: RMSD, RMSF, RDF, contacts
- Selection: MDAnalysis atom selection language
- Integration: NumPy, SciPy, parallel
Citation
Michaud-Agrawal, N. et al. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32, 2319-2327 (2011). DOI:10.1002/jcc.21787