alterlab-molecular-dynamics
CommunityRun and analyze MD simulations.
Education & Research#workflows#molecular-dynamics#protein-ligand#trajectory-analysis#mdanalysis#openmm#rmsd-rmsf
AuthorAlterLab-IEU
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Molecular dynamics simulations are powerful but require setup, execution, and analysis that can be time-consuming and error-prone.
Core Features & Use Cases
- OpenMM-based system preparation, energy minimization, NVT/NPT equilibration, and production MD for protein and small-molecule systems.
- Trajectory analysis using MDAnalysis for RMSD, RMSF, contacts, and free energy surfaces across structural biology, drug design, and biophysics scenarios.
Quick Start
Set up a protein-ligand MD workflow to automatically prepare a system, minimize energy, equilibrate, run production MD, and analyze trajectories with MDAnalysis.
Dependency Matrix
Required Modules
None requiredComponents
references
💻 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: alterlab-molecular-dynamics Download link: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/archive/main.zip#alterlab-molecular-dynamics Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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