MDAnalysis — MD Trajectory Analysis

MDAnalysis 2.10.0 (2025). Core pattern: Universe (topology + trajectory) → AtomGroup (selection) → AnalysisBase.run() → .results.

When to Use This Skill

• Loading GROMACS, AMBER, NAMD, CHARMM, LAMMPS trajectories
• RMSD and RMSF calculations (protein stability, flexibility)
• Structural alignment across trajectory frames
• Hydrogen bond detection and lifetime analysis
• Protein-ligand contacts and binding site analysis
• Dihedral angles (Ramachandran plots, chi angles)
• Secondary structure (DSSP) assignment
• PCA of conformational dynamics
• Radial distribution functions (RDF), density maps
• Mean square displacement (MSD), diffusion coefficients

Quick Start

import MDAnalysis as mda
from MDAnalysis.analysis import rms, align

# Load topology + trajectory
u = mda.Universe('protein.prmtop', 'traj.dcd')
print(u)                   # <Universe with 45000 atoms>
print(len(u.trajectory))   # number of frames

# Select atoms
protein = u.select_atoms('protein')
ca      = u.select_atoms('protein and name CA')
ligand  = u.select_atoms('resname LIG')

# Iterate trajectory
for ts in u.trajectory:
    print(ts.frame, ts.time, ca.positions.mean(axis=0))

Router — What to Read

Task	Reference
Universe, topology formats, selections, trajectory I/O, writing	references/universe-selections.md
RMSD, RMSF, alignment, radius of gyration	references/rmsd-rmsf-alignment.md
Hydrogen bonds, native contacts, binding residues	references/contacts-hbonds.md
Dihedrals, DSSP, PCA, RDF, density, MSD	references/structure-dynamics.md
Protein-ligand interaction analysis workflow	references/protein-ligand.md

Key Modules

Module	Import	Role
rms	from MDAnalysis.analysis import rms	RMSD, RMSF
align	from MDAnalysis.analysis import align	Structural alignment
contacts	from MDAnalysis.analysis import contacts	Native contacts
hydrogenbonds	from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import HydrogenBondAnalysis	H-bonds
dihedrals	from MDAnalysis.analysis.dihedrals import Ramachandran, Janin	Dihedral angles
dssp	from MDAnalysis.analysis.dssp import DSSP	Secondary structure
pca	from MDAnalysis.analysis.pca import PCA	Conformational PCA
rdf	from MDAnalysis.analysis.rdf import InterRDF	Radial distribution
density	from MDAnalysis.analysis.density import DensityAnalysis	Density maps
msd	from MDAnalysis.analysis.msd import EinsteinMSD	Diffusion
distances	from MDAnalysis.analysis.distances import dist, between	Distances

Supported Formats

Topology:  PSF, PRMTOP (Amber), GRO (GROMACS), PDB, MOL2, TPR, CRD, XML
Trajectory: DCD, XTC, TRR, NC (Amber), LAMMPSDUMP, H5MD, TNG, XYZ, PDB

Installation

pip install MDAnalysis MDAnalysisData
conda install -c conda-forge mdanalysis

# Verify
python -c "import MDAnalysis; print(MDAnalysis.__version__)"

AnalysisBase Pattern (all analysis modules)

analysis = SomeAnalysis(atomgroup, **params)
analysis.run(start=0, stop=None, step=1, verbose=True)
results = analysis.results      # dict-like Results object

Related Skills

• ase — ASE MD trajectories, structure building (complementary)
• scientific-skills:matplotlib — plotting RMSD, RMSF curves
• scientific-skills:seaborn — heatmaps for contact maps
• scientific-skills:plotly — interactive conformational space plots
• scientific-skills:biopython — PDB fetching and sequence tools