Can this skill help me run GROMACS or AMBER simulations?

No, this skill is focused on the analysis phase. It provides expert guidance on using the MDAnalysis library to process and analyze the output files generated by simulation engines like GROMACS, AMBER, and NAMD.

How does this skill handle very large trajectory files?

It enforces the 'stream-not-load' anti-pattern, guiding you to iterate through frames one-by-one using the Universe object rather than loading all coordinates into memory at once.

Does it support VMD-style atom selections?

Yes, it provides optimized patterns for the select_atoms method, which uses a syntax very similar to VMD for selecting residues, segments, or atoms within specific distances.

Why should I use this skill instead of standard Python code?

This skill integrates domain-specific biophysics knowledge, ensuring that critical steps like trajectory alignment and Periodic Boundary Condition (PBC) handling are correctly implemented to avoid common analysis errors.

Molecular Dynamics Analysis (MDAnalysis)

Name: Molecular Dynamics Analysis (MDAnalysis)
Author: tondevrel

bytondevrel

•

Data Science & ML

Analyzes molecular dynamics trajectories and structural data using the MDAnalysis Python library for biophysical research.

This skill provides specialized guidance for the MDAnalysis library, the standard Python toolkit for processing molecular dynamics simulations. It streamlines the workflow for loading various trajectory formats, performing complex atom selections using VMD-like syntax, and executing structural analyses like RMSD, RMSF, and hydrogen bond detection. By enforcing best practices such as memory-efficient frame streaming, trajectory alignment, and periodic boundary condition (PBC) awareness, this skill helps researchers and developers extract precise biophysical insights from large-scale simulation data.

Key Features

01Comprehensive trajectory loading and conversion for GROMACS, AMBER, and NAMD formats.

02Automated structural analysis including RMSD, RMSF, SASA, and dihedral calculations.

031 GitHub stars

04Memory-efficient processing patterns for handling massive multi-gigabyte trajectories.

05Periodic Boundary Condition (PBC) aware distance and spatial analysis.

06Advanced atom selection using VMD-like syntax for precise molecular filtering.

Use Cases

01Calculating protein backbone stability and conformational changes over time.

02Quantifying hydrogen bond networks and contact maps in biomolecular complexes.

03Analyzing solvent and ion distribution patterns around membrane systems or active sites.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add tondevrel/scientific-agent-skills mdanalysis

For use in Claude.ai and ChatGPT

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