molclaw-openawsem-tool

What problem does it solve?

This Skill automates running OpenAWSEM coarse-grained protein simulations and extracting representative trajectory frames so users can perform ensemble analysis and screening without manual trajectory handling.

Core Features & Use Cases

• Simulation Execution: Run OpenAWSEM annealing or NVT workflows with configurable steps, temperature, platform, and GPU selection to produce simulation outputs.
• Trajectory Extraction: Detect trajectory and topology files and extract evenly spaced or time-specified PDB frames using multiple backends (mdtraj, mdanalysis, auto).
• Reproducibility & Safety: Produces structured output directories and explicit instructions to download all structure files locally for verification; suitable for structure screening, folding studies, and downstream ensemble-based analyses.

Quick Start

Run an OpenAWSEM annealing simulation on your simulation directory and then extract 100 representative trajectory frames for downstream analysis.