Uploading Structure Files
Clavis accepts GROMACS.gro files containing water molecule trajectories.
File Requirements
Your.gro file should contain:
- Water molecules with standard residue names:
SOL,HOH,WAT, orH2O - Periodic boundary conditions (box vectors on the last line)
- One or more frames (for trajectory analysis)
Upload Process
- Click the UPLOAD .GRO button in the top toolbar
- Select your structure file
- Wait for parsing to complete
- The molecule count and frame information will appear in the sidebar
Multi-Frame Trajectories
For trajectory files with multiple frames:- Use the Timeline slider to navigate between frames
- Enable Auto-analyze to process frames as you navigate
- Use ANALYZE ALL FRAMES for batch processing
File Size Limits
| Plan | Max File Size | Max Atoms |
|---|---|---|
| Free | 50 MB | 100,000 |
| Pro | 500 MB | 1,000,000 |
Troubleshooting
File not recognized
File not recognized
Ensure your file has the
.gro extension and follows GROMACS format specifications.Parsing errors
Parsing errors
Check that your file contains valid coordinate data and properly formatted box vectors.
No water molecules detected
No water molecules detected
Verify that water residues use standard naming: SOL, HOH, WAT, or H2O.