mdanalysis

MDAnalysis - Molecular Dynamics Analysis

Python library for reading, writing, and analyzing molecular dynamics trajectories and structural files.

When to Use

• Loading MD trajectories (DCD, XTC, TRR, NetCDF, etc.)
• RMSD and RMSF calculations
• Distance, angle, and dihedral analysis
• Atom selections (VMD-like syntax)
• Hydrogen bond analysis
• Solvent Accessible Surface Area (SASA)
• Protein secondary structure analysis
• Membrane system analysis
• Water/ion distribution analysis
• Trajectory alignment and fitting
• Custom trajectory analysis
• Converting between file formats

Reference Documentation

Official docs: https://www.mdanalysis.org/docs/
Search patterns: MDAnalysis.Universe, MDAnalysis.analysis.rms, MDAnalysis.analysis.distances

Core Principles

Use MDAnalysis For

Task	Module	Example
Load trajectory	Universe	Universe(topology, trajectory)
RMSD calculation	analysis.rms	RMSD(mobile, ref)
Atom selection	select_atoms	u.select_atoms('protein')
Distance analysis	analysis.distances	distance_array(pos1, pos2)
H-bond analysis	analysis.hbonds	HydrogenBondAnalysis()
SASA calculation	analysis.sasa	SASAnalysis()
Contacts analysis	analysis.contacts	Contacts()
Trajectory writing	Writer	with Writer() as W

Do NOT Use For

• Running MD simulations (use GROMACS, AMBER, NAMD)
• Force field calculations (use OpenMM, MDTraj)
• Quantum chemistry (use PySCF, Qiskit)
• Protein structure prediction (use AlphaFold, RosettaFold)
• Initial structure building (use Biopython, PyMOL)

Quick Reference

Installation

# pip
pip install MDAnalysis

# With additional analysis modules
pip install MDAnalysis[analysis]

# conda
conda install -c conda-forge mdanalysis

# Development version
pip install git+https://github.com/MDAnalysis/mdanalysis.git

Standard Imports

# Core imports
import MDAnalysis as mda
from MDAnalysis import Universe
from MDAnalysis.analysis import rms, align, distances

# Common analysis modules
from MDAnalysis.analysis.rms import RMSD, RMSF
from MDAnalysis.analysis.distances import distance_array
from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import HydrogenBondAnalysis
from MDAnalysis.analysis.dihedrals import Dihedral

# Utilities
import numpy as np
import matplotlib.pyplot as plt