Automatic GROMACS Workflow

Start automatic continuation

Complete the Structure Repair inspection and select the ligand first. From that point, this page can automatically queue ligand parameterisation, complex validation, solvation, equilibration, production MD and trajectory analysis.

One review remains mandatory: the software will not guess the ligand identity, formal charge, stereochemistry, bond orders, retained cofactors, or whether missing loops should be built.

Structure-repair jobAutomatic-workflow project nameLigand residue/base nameOptional SDF/MOL2 chemistry fileSDF or MOL2 is preferred because it preserves bond orders.Formal net chargeMultiplicityLigand atom typesCharge methodProtein force fieldWater modelBox typeBox distance (nm)

MD settings

Temperature (K)Pressure (bar)NaCl (mol/L)NVT duration (ps)NPT duration (ps)Production duration (ns)Trajectory interval (ps)Compute modeOpenMP threads (0 = automatic)

Run production MD after successful NPT. Run the complete analysis suite after production: protein and ligand stability, interactions, PCA/clustering, MM/GBSA and MM/PBSA.

I reviewed the ligand identity, charge, stereochemistry and bond orders. I understand that the workflow stops at any failed validation and that long MD runs can take hours or days.

Recent automatic workflows

Project	Status	Stage	Progress	Created
Pilot_2_md	failed	analysis failed	90.6%	2026-07-13 12:44:08	Open
Pilot_1_md	completed	completed	100.0%	2026-07-13 06:00:10	Open
Pilot_1_Ligand	completed	completed	100.0%	2026-07-13 05:41:05	Open