How are the analysis results presented?

The skill provides a structured report summarizing stability metrics, key observations on flexible regions, and recommendations for further simulation steps.

Does it support ligand interaction analysis?

Yes, it includes tools for protein-ligand hydrogen bonds and contact analysis to characterize binding behavior and solvation shells.

Can this skill identify if a simulation has failed?

Yes, it monitors for warning signs like continuously increasing RMSD, energy spikes, or temperature drift that indicate instability or incorrect parameters.

What file formats are required for MD Analyze?

It typically requires an Amber topology file (parm7) and a trajectory file (DCD or similar) generated during the MD simulation phase.

MD Trajectory Analysis

Name: MD Trajectory Analysis
Author: matsunagalab

bymatsunagalab

•

Ciencia de Datos y ML

Analyzes and interprets molecular dynamics simulation trajectories using MDClaw CLI tools to evaluate structural stability and molecular interactions.

The MD Analyze skill empowers researchers and computational biophysicists to extract meaningful insights from molecular dynamics simulations. By leveraging the MDClaw CLI, it automates the calculation of essential metrics such as RMSD, RMSF, hydrogen bonding, and secondary structure changes. It provides expert-level interpretation of simulation quality, identifying signs of stability or equilibration issues, and generates comprehensive summaries that cover system behavior, structural fluctuations, and energy convergence to ensure valid scientific results.

Características Principales

01Secondary structure and radius of gyration calculations

02Structural stability analysis via RMSD and RMSF metrics

031 GitHub stars

04Comprehensive hydrogen bond and residue contact mapping

05Automated interpretation of simulation quality indicators and warnings

06Energy timeseries analysis and convergence monitoring

Casos de Uso

01Identifying flexible loop regions and rigid structural cores via fluctuation analysis

02Characterizing binding stability through protein-ligand interaction analysis

03Evaluating the equilibration and convergence of a protein simulation in water

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add matsunagalab/mdclaw md-analyze

For use in Claude.ai and ChatGPT

Download Skill