Automate MD equilibration workflows from minimization through NPT steps.
npx skills add https://github.com/matsunagalab/mdclaw --skill md-equilibration
Please help me install this Agent Skill. Skill: MD Equilibration Source: https://github.com/matsunagalab/mdclaw/tree/main/skills/md-equilibration Command: npx skills add https://github.com/matsunagalab/mdclaw --skill md-equilibration
Equilibrates a prepared MD system by performing energy minimization, NVT heating, and NPT density equilibration, producing a production-ready checkpoint (equilibrated.chk) for handoff to MD production.
Create an eq node for your job and start the equilibration workflow using MDClaw.
High-intent search queries and answers about installing and using this skill.
You can automate MD equilibration by running a single DAG-based workflow that executes energy minimization, NVT heating, and NPT density stabilization, producing an equilibrated checkpoint for production handoff.
The standard MD equilibration sequence involves energy minimization followed by NVT heating and NPT density equilibration, which stabilizes the prepared system before generating a production-ready checkpoint.
Yes, you can configure temperature, pressure, and seed parameters during NVT heating and NPT density equilibration, with adjustable parameters and safeguards to ensure reproducible MD equilibration results.
Yes, the MD equilibration workflow explicitly targets both explicit-water and implicit-solvent DAG workflows, guiding them through energy minimization, NVT heating, and NPT steps with error handling.
You hand off the equilibrated MD system by creating a dedicated equilibration job-dir node that generates an equilibrated.chk checkpoint, which seamlessly progresses into MD production within the DAG workflow.
The NPT density equilibration process includes adjustable parameter configurations and error handling safeguards for job-dir node creation and parameter persistence to ensure stable MD equilibration.
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