MD Prepare
OfficialAutomate MD preparation with MDClaw CLI.
Education & Research#automation#topology#molecular-dynamics#solvation#structure-preparation#mdclaw#ligand-parameterization
Authormatsunagalab
Version1.0.0
Installs0
System Documentation
What problem does it solve?
MDPrepare automates end-to-end molecular dynamics preparation workflows for researchers, orchestrating structure acquisition, chain/ligand selection, structure cleaning, solvation, and topology generation using the MDClaw CLI.
Core Features & Use Cases
- End-to-end MD prep: structure acquisition, cleaning, solvation, and topology generation for single-system DAG workflows.
- Explicit-water and implicit-solvent workflows with metal-ion handling and ligand parameterization.
- Deterministic defaults and robust checks to support HITL decisions and reproducibility.
Quick Start
Provide the target structure and run the MDPrepare flow to produce a solvated, topology-ready system.
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 Prepare Download link: https://github.com/matsunagalab/mdclaw/archive/main.zip#md-prepare Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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