molclaw-goca-tool

What problem does it solve?

This Skill automates the setup, execution, and artifact collection for GoCa coarse-grained molecular dynamics runs on protein structures, eliminating manual orchestration of preprocessing, MD execution, and output tracking so researchers can reliably produce and retrieve structural trajectories and configuration artifacts.

Core Features & Use Cases

• Integrated GoCa execution: Launches the GoCa coarse-grained pipeline with options for full MD, energy minimization, and post-processing using configurable temperature, MD time, and GPU IDs.
• Artifact organization & retrieval: Produces a run-specific output directory with normalized key files (Cα trajectory PDBs, configuration files, analysis directories) and explicit instructions to download all structure outputs for downstream processing.
• Dry-run and reproducibility: Supports a dry_run mode that creates tracked run directories and returns normalized parameters without executing simulations, enabling reproducible pipelines and inspection before committing compute resources.
• Use Case: Relax a target protein, generate a coarse-grained trajectory for subsequent full-atom reconstruction, and collect all Cα PDBs and config files for off-server analysis.

Quick Start

Run the goca_pipeline tool on the uploaded protein PDB in dry-run mode to create a tracked run directory and list the key output files.