molecular-dynamics-guide
CommunitySet up, run, and analyze MD simulations.
Education & Research#trajectory analysis#gromacs#molecular dynamics#mdanalysis#openmm#md simulations#force fields
Authorliongkj
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Molecular dynamics simulations require careful setup, parameterization, and rigorous trajectory analysis. This skill provides a structured guide to prepare systems, select force fields, run simulations, and interpret results.
Core Features & Use Cases
- System preparation and force-field setup for biomolecular systems
- Workflow examples for GROMACS and OpenMM
- Trajectory analysis with MDAnalysis and RMSD/RG metrics
- Basic free energy calculation concepts and methods
Quick Start
Set up a simple protein system, run a short MD trajectory, and perform a basic trajectory analysis.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: molecular-dynamics-guide Download link: https://github.com/liongkj/zotero-library-bridge-skills/archive/main.zip#molecular-dynamics-guide Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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