Mdanalysis

Claude Plugin for CompChem , Drug Discovery & Organic Chemistry reasoning

Install

npx -y skills add Kdevos12/ALKYL --skill mdanalysis

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Use when analyzing molecular dynamics trajectories with MDAnalysis. Covers Universe/AtomGroup, RMSD/RMSF/alignment, contacts and hydrogen bonds, dihedral/secondary structure/PCA analysis, and protein-ligand binding analysis.

SKILL.md

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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