Galaxy | Tool Preview

GROMACS initial setup (version 2022+galaxy0)
Input structure
Model for simulating water molecules in the solvent
Specify a molecular force field
Ignore hydrogen atoms that are in the coordinate file.
Generate detailed log information that can be summarized with ParseLog.

What it does

This tool performs the initial setup prior to a GROMACS simulation. This entails producing a topology from an input structure using the pdb2gmx command.

Please note that the tool will only successfully generate a topology for residues it recognizes (i.e. standard amino acids). If the structure contains other components such as ligands, these should be separately parameterized with the AmberTools or ACPYPE tools. In this case, make sure to also use an AMBER forcefield for this tool to ensure compatability with the ligand topology.


  • PDB file.
  • Water model and forcefield must be specified.


  • GROMACS topology (TOP) file.
  • Position restraint (itp) file, which may be useful for system equilibration.
  • GRO structure file.