{"id":21890577,"url":"https://github.com/pritampanda15/gromacs-command-finder","last_synced_at":"2026-05-01T03:33:55.059Z","repository":{"id":264183624,"uuid":"892597157","full_name":"pritampanda15/Gromacs-Command-Finder","owner":"pritampanda15","description":"Gromacs Command Finder is a tool to search for gromacs specific comands like topology, trajectory analysis, PME, etc.","archived":false,"fork":false,"pushed_at":"2025-03-21T19:44:37.000Z","size":54,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-02-06T11:34:12.966Z","etag":null,"topics":["ai","flask","gemini","llm","python","rapidfuzz"],"latest_commit_sha":null,"homepage":"https://gromacs-command-finder-pwnaf8a8qgxleesb7m4d5h.streamlit.app/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pritampanda15.png","metadata":{"files":{"readme":"Readme.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-11-22T12:17:12.000Z","updated_at":"2025-10-23T12:22:10.000Z","dependencies_parsed_at":"2025-01-26T21:30:53.591Z","dependency_job_id":"64624977-3632-4f4e-ab25-2bb1616b921d","html_url":"https://github.com/pritampanda15/Gromacs-Command-Finder","commit_stats":null,"previous_names":["pritampanda15/gromacs-command-finder"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/pritampanda15/Gromacs-Command-Finder","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pritampanda15%2FGromacs-Command-Finder","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pritampanda15%2FGromacs-Command-Finder/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pritampanda15%2FGromacs-Command-Finder/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pritampanda15%2FGromacs-Command-Finder/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pritampanda15","download_url":"https://codeload.github.com/pritampanda15/Gromacs-Command-Finder/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pritampanda15%2FGromacs-Command-Finder/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32484352,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-30T13:12:12.517Z","status":"online","status_checked_at":"2026-05-01T02:00:05.856Z","response_time":64,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["ai","flask","gemini","llm","python","rapidfuzz"],"created_at":"2024-11-28T12:15:56.313Z","updated_at":"2026-05-01T03:33:55.032Z","avatar_url":"https://github.com/pritampanda15.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"### Access to the App: https://gromacs-command-finder-pwnaf8a8qgxleesb7m4d5h.streamlit.app/\n\n\n### **Categories for GROMACS Commands**\n\n#### **1. General Simulation Setup**\n- Build topology of protein\n- Build topology of ligand\n- Build unit cell\n- Generate solvent box\n- Add ions\n- Equilibrate system (NVT)\n- Equilibrate system (NPT)\n- Prepare molecular dynamics\n- Run production MD simulation\n- Convert trajectory format\n\n#### **2. Energy Minimization and Molecular Dynamics**\n- Energy minimization\n- Position restraint energy minimization\n- Restrained MD simulation\n- Temperature coupling group setup\n- Pressure coupling group setup\n- Pulling simulation setup\n- Extend MD simulation\n- Run simulation on multiple GPUs\n\n#### **3. Trajectory Analysis**\n- Analyze RMSD\n- Calculate RMSF\n- Compute radius of gyration\n- Calculate hydrogen bonds\n- Remove periodic boundary conditions\n- Fit trajectory to reference\n- Convert trajectory types\n- Check trajectory periodicity\n- Analyze diffusion coefficients\n- RMSF per residue\n- Principal component time series\n- Generate per-frame snapshots\n\n#### **4. Structural Analysis**\n- Analyze secondary structure\n- Cluster analysis\n- Generate Ramachandran plot\n- Calculate dihedral angles\n- Hydrogen bond lifetime analysis\n- Analyze molecular contacts\n- Analyze lipid headgroup orientation\n- Extract specific residues\n- Analyze solvent shell around solute\n\n#### **5. Solvent and Membrane Analysis**\n- Generate solvent-accessible surface area (SASA)\n- Compute RDF (radial distribution function)\n- Analyze solvent density\n- Analyze solvent orientation\n- Compute membrane thickness\n- Analyze lipid order parameters\n- Calculate solvent accessible volume\n- Measure water orientation\n\n#### **6. Free Energy and Binding Analysis**\n- Calculate potential of mean force (PMF)\n- Free energy difference via BAR\n- Ligand binding energy calculation\n- Protein-ligand binding energy\n- Weighted histogram analysis (WHAM)\n- Analyze free energy landscapes\n\n#### **7. Visualization and Export**\n- Visualize trajectory in PDB format\n- Generate density map for ions\n- Create secondary structure timelines\n- Export data to CSV\n- Generate XPM plots\n- Generate trajectory movies\n\n#### **8. Advanced Molecular Dynamics and QM/MM**\n- Backmap coarse-grained to atomistic\n- Set up QM/MM simulation\n- Analyze QM/MM interaction energies\n- Transition state search in QM/MM\n- Calculate QM/MM polarization energies\n\n#### **9. Specialized Analysis**\n- Compute Lennard-Jones potential\n- Generate solvent density map\n- Analyze interfacial tension\n- Analyze hydrophobic clustering\n- Protein unfolding pathway analysis\n- Analyze beta-sheet interactions\n- Compute salt bridges\n- Analyze helical content\n- Compute dielectric constants\n\n#### **10. Debugging and Optimization**\n- Check TPR file\n- Verify trajectory integrity\n- Benchmark custom hardware\n- Tune PME grid\n- Estimate PME error\n- Optimize PME load balancing\n\n#### **11. Rare Commands**\n- Detect water chain formation\n- Calculate bond angle distribution\n- Measure mismatch repair events\n- Analyze RNA folding dynamics\n- Visualize electric field around system\n- Analyze membrane curvature\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpritampanda15%2Fgromacs-command-finder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpritampanda15%2Fgromacs-command-finder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpritampanda15%2Fgromacs-command-finder/lists"}