gromacs-protein-analysis

What This Skill Does

The gromacs-protein-analysis skill acts as an expert companion for researchers performing molecular dynamics simulations using the GROMACS suite. It encapsulates deep domain knowledge about protein trajectory post-processing and statistical analysis. The skill is designed to guide the Agent through the lifecycle of a protein analysis project, ensuring that dependencies between analyses—such as performing PBC correction before any geometric calculations—are strictly followed. It provides a comprehensive workflow covering nine essential methodologies including RMSD for stability monitoring, RMSF for residue-level flexibility, SASA for solvent exposure, and FEL for energy landscape mapping. Additionally, it features built-in platform compatibility intelligence, ensuring users on Linux, macOS, or Windows CMD can successfully execute GROMACS commands through proper piping and input redirection.

Installation

You can integrate this skill into your OpenClaw environment by running the following command in your terminal: clawhub install openclaw/skills/skills/charleshahn/gromacs-protein-analysis

Use Cases

This skill is ideal for:

1. Automating the standard post-processing pipeline for GROMACS simulation outputs.
2. Troubleshooting common simulation errors such as periodicity artifacts or unstable RMSD plots.
3. Extracting complex insights from large trajectory files, such as dynamic correlation between distant protein domains (DCCM).
4. Standardizing reporting for biochemical research papers by generating consistent plots for RMSF, SASA, and free energy landscapes.

Example Prompts

1. "I've just finished my 500ns MD simulation. Walk me through the standard workflow to check if my protein has equilibrated using RMSD and Gyrate analysis."
2. "My simulation keeps showing artifacts at the periodic boundaries. How do I fix the trajectory using the gromacs-protein-analysis skill?"
3. "After calculating the PCA of my trajectory, how can I use that to generate a Free Energy Landscape (FEL) map?"

Tips & Limitations

• Dependencies: Always perform PBC correction (trjconv) as the first step. Analytical steps like FEL are dependent on prior calculations like PCA or RMSD/Gyrate; ensure these are generated first.
• Cross-Platform: Always verify your OS environment. The skill documentation provides specific command-line variations for Windows CMD users compared to Linux/Bash. If you are unsure, default to using WSL or Git Bash for maximum compatibility with GROMACS pipe inputs.
• Resource Usage: Note that PCA and DCCM calculations on long trajectories can be computationally intensive and memory-heavy; ensure your system has sufficient RAM before triggering these commands.