GROMACS

Overview

Protein-only PDB relaxation before downstream modeling.
Running an already prepared coordinate/topology/MDP system.
Executing or continuing a compiled TPR simulation.
Collecting standard GROMACS outputs for local analysis.

Modes

Mode	Input shape	When to use it
`protein_relaxation` Protein Relaxation Default	Uses one selected file/source when file parameters are present.	Build a solvated protein system from one PDB, add optional NaCl ions, and run energy minimization.
`prepared_system` Prepared System	Uses one selected file/source when file parameters are present.	Compile a prepared coordinate/topology/MDP set into a run input file and run it.
`run_input` Run TPR	Uses one selected file/source when file parameters are present.	Run an existing GROMACS .tpr file, with optional checkpoint continuation.

Canonical Job Configuration

These are the fields exposed by the default job configuration for gromacs. They are also returned by GET /api/v1/program/params?program=gromacs and submitted as the params JSON object to POST /api/v1/job/submit.

Parameter	Type	Modes	What it does
`output_name` Output Name	Text	All modes	Used as the result file prefix.
`protein_structure` Protein PDB	Structure file	Protein Relaxation	Protein-only PDB. Ligands, custom residues, covalent modifications, and membranes need advanced GROMACS control. Required; Files: .pdb
`force_field_water` Force Field	Text	Protein Relaxation	Bundled protein force-field and water-model pairing used by pdb2gmx. Default: AMBER99SB-ILDN/TIP3P; Options: AMBER99SB-ILDN/TIP3P, CHARMM27/TIP3P
`box_shape` Box Shape	Text	Protein Relaxation	Dodecahedron is compact for globular proteins; cubic is simpler but larger. Default: Dodecahedron; Options: Dodecahedron, Cubic, Octahedron
`solvent_padding_nm` Solvent Padding (nm)	Number	Protein Relaxation	Minimum distance from the protein to the box edge before solvation. Default: 1; Range: 0.5-3
`ion_treatment` Ions	Text	Protein Relaxation	Neutralization replaces solvent with NA/CL ions; custom salt adds NaCl at the requested molarity. Default: Neutralize + 0.15 M NaCl; Options: Neutralize + 0.15 M NaCl, Neutralize Only, Neutralize + Custom NaCl
`custom_salt_molar` NaCl Concentration (M)	Number	Protein Relaxation	Default: 0.15; Range: 0-1; Shown when ion_treatment is Neutralize + Custom NaCl
`relaxation_depth` Relaxation Depth	Text	Protein Relaxation	Controls the energy minimization convergence target and default step budget. Default: Standard; Options: Quick, Standard, Tight
`coordinate_file` Coordinates	Input file	Prepared System	Prepared coordinates matching the topology and MDP. Required; Files: .gro, .pdb, .g96
`topology_file` Topology	Input file	Prepared System	Topology must be self-contained or use include paths that grompp can resolve. Required; Files: .top
`mdp_file` MDP Parameters	Input file	Prepared System	Simulation or minimization parameters for grompp. Required; Files: .mdp
`tpr_file` Run Input	Input file	Run TPR	Portable run input file produced by grompp. Required; Files: .tpr

Advanced configuration fields

Parameter	Type	Modes	What it does
`position_restraints` Position Restraints	Yes/no	Protein Relaxation	Keeps protein atoms near their starting positions while solvent and ions relax. Default: true
`rebuild_hydrogens` Rebuild Hydrogens	Yes/no	Protein Relaxation	Ignore input hydrogens and rebuild them from the selected force field. Default: true
`max_minimization_steps` Max Minimization Steps	Integer	Protein Relaxation	depth default Range: 100-500000
`index_file` Index File	Input file	Prepared System	Files: .ndx
`checkpoint_file` Checkpoint	Input file	Run TPR	Optional checkpoint for continuation; the job form writes a fresh output part. Files: .cpt
`step_limit` Step Limit	Integer	Prepared System, Run TPR	0 uses the step count in the MDP/TPR. Positive values override the run input step count. Default: 0; Range: 0-1000000000

Outputs And Metrics

Logs, final coordinates, energy files, trajectories, TPR files, processed MDP files, topology files, and checkpoints when written.
For minimization, inspect final potential energy, maximum force, and warnings.
For MD, inspect completed steps, temperature, pressure, energy terms, and preprocessing warnings.

Common Examples

Protein cleanup: AMBER99SB-ILDN/TIP3P, dodecahedron, 1.0 nm padding, neutralize plus 0.15 M NaCl, Standard minimization.
Production run: prepared GRO, TOP, and MDP files with Step Limit 0.
Restart: Run TPR with matching CPT checkpoint.

Example API params

{
  "mode": "protein_relaxation",
  "protein_structure": "protein.pdb",
  "force_field_water": "AMBER99SB-ILDN/TIP3P",
  "box_shape": "Dodecahedron",
  "ion_treatment": "Neutralize + 0.15 M NaCl"
}

Caveats

Protein Relaxation does not parameterize ligands, metals, covalent modifications, membranes, or novel residues.
Treat grompp warnings seriously.
A checkpoint should match the same run input and simulation state.

Advanced Submit

Advanced submit is still available for direct program arguments through POST /api/v1/job/submit-advanced. Prefer canonical configuration unless you need exact low-level arguments or are reproducing a known command line.

Advanced submit accepts one GROMACS command per args entry for full command-line workflows.
Commands should use uploaded inputs and write outputs intended for download; avoid shell operators.

curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer <api_key>" \
  -F program=gromacs \
  -F 'params={"mode":"protein_relaxation","protein_pdb":"protein.pdb","force_field":"AMBER99SB-ILDN/TIP3P","box_shape":"Dodecahedron","ions":"Neutralize + 0.15 M NaCl"}'