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ase-atomistic

Runs atomistic simulations including geometry optimization, NEB, and molecular dynamics with trajectory analysis.

33|6|Updated Mar 17, 2026
Search Tags:#geometry-optimization#molecular-dynamics#ase#rdf#trajectory-analysis#neb#atomistic-simulation
One-click install
npx skills add https://github.com/xjtulyc/awesome-rosetta-skills --skill ase-atomistic
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ase-atomistic
Source: https://github.com/xjtulyc/awesome-rosetta-skills/tree/main/skills/02-chemistry/ase-atomistic
Command: npx skills add https://github.com/xjtulyc/awesome-rosetta-skills --skill ase-atomistic

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires ase, numpy, scipy, matplotlib.

What problem does it solve?

This Skill helps you create and run atomistic simulations by turning atomic structures into actionable calculations for relaxation, transition states, dynamics, and post-processing analysis.

Core Features & Use Cases

  • Structure building: Generate bulk, surfaces, molecules, and clusters for simulation-ready atomic models.
  • Geometry optimization: Relax structures using force-based minimization with common optimizers and optional constraints.
  • Reaction pathways and dynamics: Find minimum energy paths via NEB and simulate time evolution with molecular dynamics.
  • Trajectory and property analysis: Compute and visualize RDF, MSD, and RMSD from generated trajectories, plus run vibration calculations for molecules (numerical Hessian workflows).
  • Use Case: Create a Pt(111) surface model, relax it, adsorb a CO molecule at multiple sites, compare adsorption energies, and identify the most stable configuration.

Quick Start

Use the ase-atomistic skill to set up an ASE model for a surface plus adsorbate, run geometry relaxations with constraints, and compute energies to estimate adsorption stability.

Frequently Asked Questions about ase-atomistic

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I calculate adsorption energies on a specific surface using ASE?▼

You can build a surface model, run geometry relaxations with fixed atom constraints, and compute energies to estimate adsorption stability for configurations like CO on Pt(111).

How do I compute RDF, MSD, and RMSD from molecular dynamics trajectories?▼

You run molecular dynamics to generate trajectory frames, then apply post-processing and statistical normalization to compute and visualize RDF, MSD, and RMSD values.

Can I find reaction pathways and transition states with NEB in ASE?▼

Yes, you can find minimum energy paths and transition states by running NEB transition-state searches between two atomic configurations to estimate reaction pathways.

Does this ASE workflow support geometry optimization with fixed atoms?▼

Yes, it performs geometry optimization by relaxing structures with force-based minimization and supports applying optional constraints to fix specific atoms.

What atomistic calculators do I need to run these simulations?▼

You need an ASE-centered Python execution environment with atomistic calculators like EMT to provide the energy and force computations for optimization and dynamics.

How do I perform vibration calculations for molecules in ASE?▼

You can run vibration calculations for molecules using numerical Hessian workflows to compute vibrational frequencies by evaluating energy derivatives with respect to atomic displacements.

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