MD Analyze
OfficialEfficient trajectory consolidation and analysis.
Authormatsunagalab
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Automatically consolidates fragmented MD trajectories from a prod lineage into a single, memory-efficient combined trajectory and provides a reference structure for downstream analysis.
Core Features & Use Cases
- Trajectory consolidation: streaming concatenation of prod trajectories with user-selected atom subsets and stride.
- Artifact generation: outputs combined_trajectory (dcd), reference_pdb, and selection_indices for cross-tool comparisons.
- Handoff-ready data: supplies metadata (n_atoms_selected, total_frames, frames_per_source, source_trajectories, prmtop_file) for RMSD, RMSF, and distance analyses.
Quick Start
Run the MD Analyze workflow to concatenate the prod trajectory lineage into a single combined trajectory and generate a reference structure for downstream analyses.
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: MD Analyze Download link: https://github.com/matsunagalab/mdclaw/archive/main.zip#md-analyze Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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