Access to the App: https://gromacs-command-finder-a9630d013893.herokuapp.com/

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