Unified workspace

GROMACS simulation dashboard

Use one guided route for protein–ligand simulations. Manual pages remain available only under Advanced tools for troubleshooting.

Start
Upload the protein–ligand complex and inspect the structure.

Review once
Select the ligand and approve cleanup decisions.

Continue automatically
Ligand setup, MD preparation, production and analysis run through one workflow.

Main function

New protein–ligand simulation

This is the correct starting point for a complex such as protein + JZ4.

Start new simulation

Track progress

Automatic workflows

Check current stage, errors and completed steps from one page.

Open workflows

Outputs

Results

Open completed workflows and their repair, ligand, MD and analysis results.

Open results

Action required

Nothing is waiting for your input.

Active workflows

No automatic workflow is currently running.

What should I use?

For normal protein–ligand work, use only: New simulation → Automatic workflows → Results.

Structure Repair, Ligand Setup, Protein Wizard and Analysis are retained as advanced/manual tools. They should not be used separately unless a workflow stops and you are diagnosing that specific stage.