alterlab-molecular-dynamics
byalterlab-ieu· 90 skills
Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis — setting up protein and small-molecule systems, assigning force fields, running energy minimization and production MD, and analyzing trajectories (RMSD, RMSF, contact maps, free energy surfaces). Use when simulating protein or ligand dynamics, equilibrating a system, or computing trajectory metrics for structural biology, drug binding, or biophysics. Part of the AlterLab Academic Skills suite.
How to install alterlab-molecular-dynamics?
alterlab-ieu/alterlab-academic-skills/alterlab-molecular-dynamics
$npx -y skills add alterlab-ieu/alterlab-academic-skills --skill alterlab-molecular-dynamicsInstalls into the current project.
›Prefer a prompt? Paste this to your agent
Run `npx skills use "https://github.com/alterlab-ieu/alterlab-academic-skills" --skill "alterlab-ieu/alterlab-academic-skills/alterlab-molecular-dynamics"` and follow the generated skill instructions now. Read its complete output, redirecting it to a temporary file first if necessary. Resolve relative paths from the supporting-files directory it provides.
Use the skills in "https://github.com/alterlab-ieu/alterlab-academic-skills" that are relevant to the current task. Run `npx skills add "https://github.com/alterlab-ieu/alterlab-academic-skills"` and select the relevant skills, then follow their instructions.
Related
6 picksType
- azure-kustoQuery and analyze data in Azure Data Explorer (Kusto/ADX) using KQL for log analytics, telemetry, and time series analysis.Jul 2026
- analyticsWhen the user wants to set up, improve, or audit analytics tracking and measurement.Jul 2026
- firecrawl-dashboard-reportingPull metrics from analytics dashboards and internal web tools with Firecrawl browser.Jun 2026
- data-storytellingTransform data into compelling narratives using visualization, context, and persuasive structure.Jul 2026
- data-visualizationCreate effective data visualizations with Python (matplotlib, seaborn, plotly).Jul 2026
- extension-oqlMake a canister's data queryable by the Caffeine Data Intelligence agent.Jul 2026
