Run production MD simulations from equilibrated checkpoints via MDClaw CLI.
npx skills add https://github.com/matsunagalab/mdclaw --skill md-production
Please help me install this Agent Skill. Skill: MD Production Source: https://github.com/matsunagalab/mdclaw/tree/main/skills/md-production Command: npx skills add https://github.com/matsunagalab/mdclaw --skill md-production
Running production molecular dynamics simulations is complex and error-prone, requiring careful management of equilibrated checkpoints, HPC submission, and toolchains. This skill provides an automated end-to-end workflow to streamline production runs from eq checkpoints.
Start a production run by selecting a completed eq node and issuing the appropriate mdclaw command to generate a prod node and run the desired simulation time.
High-intent search queries and answers about installing and using this skill.
To run production molecular dynamics simulations from an equilibrated checkpoint, select a completed eq node and issue the appropriate mdclaw command to generate a prod node and run the desired simulation time.
Yes, this production MD workflow supports HPC submission, including checkpoint restart and DAG-based node management across eq and prod nodes, using HPC-ready workflows.
Yes, you can use OpenMM backends for explicit and implicit solvent production workflows, managed through the MDClaw CLI with configurable execution modes.
The best way to restart a production MD run from a checkpoint is using the safe restart logic provided by the DAG-based node management, which handles checkpoint-based restarts across eq and prod nodes.
Yes, you need the MDClaw CLI to manage node-based production MD workflows, as it handles the creation of prod nodes, checkpoint restarts, and optional HPC submission.
Yes, there are configurable execution modes to handle autonomous or human-in-the-loop workflows, providing clear guidance for extension from existing eq/prod branches.
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