https://github.com/pritampanda15/gromacs-command-finder
Gromacs Command Finder is a tool to search for gromacs specific comands like topology, trajectory analysis, PME, etc.
https://github.com/pritampanda15/gromacs-command-finder
ai flask gemini llm python rapidfuzz
Last synced: about 2 months ago
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Gromacs Command Finder is a tool to search for gromacs specific comands like topology, trajectory analysis, PME, etc.
- Host: GitHub
- URL: https://github.com/pritampanda15/gromacs-command-finder
- Owner: pritampanda15
- Created: 2024-11-22T12:17:12.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-03-21T19:44:37.000Z (over 1 year ago)
- Last Synced: 2026-02-06T11:34:12.966Z (5 months ago)
- Topics: ai, flask, gemini, llm, python, rapidfuzz
- Language: Python
- Homepage: https://gromacs-command-finder-pwnaf8a8qgxleesb7m4d5h.streamlit.app/
- Size: 52.7 KB
- Stars: 3
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: Readme.md
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README
### Access to the App: https://gromacs-command-finder-pwnaf8a8qgxleesb7m4d5h.streamlit.app/
### **Categories for GROMACS Commands**
#### **1. General Simulation Setup**
- Build topology of protein
- Build topology of ligand
- Build unit cell
- Generate solvent box
- Add ions
- Equilibrate system (NVT)
- Equilibrate system (NPT)
- Prepare molecular dynamics
- Run production MD simulation
- Convert trajectory format
#### **2. Energy Minimization and Molecular Dynamics**
- Energy minimization
- Position restraint energy minimization
- Restrained MD simulation
- Temperature coupling group setup
- Pressure coupling group setup
- Pulling simulation setup
- Extend MD simulation
- Run simulation on multiple GPUs
#### **3. Trajectory Analysis**
- Analyze RMSD
- Calculate RMSF
- Compute radius of gyration
- Calculate hydrogen bonds
- Remove periodic boundary conditions
- Fit trajectory to reference
- Convert trajectory types
- Check trajectory periodicity
- Analyze diffusion coefficients
- RMSF per residue
- Principal component time series
- Generate per-frame snapshots
#### **4. Structural Analysis**
- Analyze secondary structure
- Cluster analysis
- Generate Ramachandran plot
- Calculate dihedral angles
- Hydrogen bond lifetime analysis
- Analyze molecular contacts
- Analyze lipid headgroup orientation
- Extract specific residues
- Analyze solvent shell around solute
#### **5. Solvent and Membrane Analysis**
- Generate solvent-accessible surface area (SASA)
- Compute RDF (radial distribution function)
- Analyze solvent density
- Analyze solvent orientation
- Compute membrane thickness
- Analyze lipid order parameters
- Calculate solvent accessible volume
- Measure water orientation
#### **6. Free Energy and Binding Analysis**
- Calculate potential of mean force (PMF)
- Free energy difference via BAR
- Ligand binding energy calculation
- Protein-ligand binding energy
- Weighted histogram analysis (WHAM)
- Analyze free energy landscapes
#### **7. Visualization and Export**
- Visualize trajectory in PDB format
- Generate density map for ions
- Create secondary structure timelines
- Export data to CSV
- Generate XPM plots
- Generate trajectory movies
#### **8. Advanced Molecular Dynamics and QM/MM**
- Backmap coarse-grained to atomistic
- Set up QM/MM simulation
- Analyze QM/MM interaction energies
- Transition state search in QM/MM
- Calculate QM/MM polarization energies
#### **9. Specialized Analysis**
- Compute Lennard-Jones potential
- Generate solvent density map
- Analyze interfacial tension
- Analyze hydrophobic clustering
- Protein unfolding pathway analysis
- Analyze beta-sheet interactions
- Compute salt bridges
- Analyze helical content
- Compute dielectric constants
#### **10. Debugging and Optimization**
- Check TPR file
- Verify trajectory integrity
- Benchmark custom hardware
- Tune PME grid
- Estimate PME error
- Optimize PME load balancing
#### **11. Rare Commands**
- Detect water chain formation
- Calculate bond angle distribution
- Measure mismatch repair events
- Analyze RNA folding dynamics
- Visualize electric field around system
- Analyze membrane curvature