OpenMM

Overview

Relax predicted or experimental structures before inspection.
Add hydrogens, explicit solvent, and ions to standard biomolecular systems.
Run short constant-temperature MD sanity checks.
Continue systems prepared externally in AMBER or GROMACS format.

Modes

Mode	Input shape	When to use it
`structure_md` Standard Structure MD Default	Uses one selected file/source when file parameters are present.	Prepare a standard biomolecular PDB/mmCIF with Amber force fields, then minimize or run MD.
`amber_md` AMBER System MD	Uses one selected file/source when file parameters are present.	Run a pre-parameterized AMBER prmtop/inpcrd-style system.
`gromacs_md` GROMACS System MD	Uses one selected file/source when file parameters are present.	Run a pre-parameterized GROMACS gro/top system with topology includes mounted beside the .top file.

Canonical Job Configuration

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

Parameter	Type	Modes	What it does
`structure` Structure	Structure file	Standard Structure MD	Choose a standard biomolecular PDB or mmCIF file. Nonstandard residues, covalent ligands, and molecules without selected-force-field parameters need advanced script mode or prepared AMBER/GROMACS inputs. Required; Files: .pdb, .cif, .mmcif
`biomolecule_force_field` Biomolecule Model	Text	Standard Structure MD	Built-in Amber biomolecular parameter set for standard proteins, nucleic acids, and compatible lipids. Default: Amber19; Options: Amber19, Amber14
`solvent_setup` Solvent Setup	Text	Standard Structure MD	Choose whether the recipe should add water and ions, use an existing periodic solvent box, or treat the structure as dry/nonperiodic. Default: Add explicit water box; Options: Add explicit water box, Use existing periodic solvent, Vacuum or dry structure
`water_model` Water Model	Text	Standard Structure MD	Water and ion parameter family used for added or already-present explicit solvent. Default: TIP3P-FB; Options: TIP3P-FB, TIP3P; Shown when solvent_setup is one of Add explicit water box, Use existing periodic solvent
`solvent_padding_nm` Water Padding	Number	Standard Structure MD	Minimum nanometers of water between the solute and box edge. Default: 1; Range: 0.5-2.5; Shown when solvent_setup is Add explicit water box
`salt_molar` Salt Concentration	Number	Standard Structure MD	Target molar salt concentration for added monovalent ions, after neutralization. Default: 0.15; Range: 0-1; Shown when solvent_setup is Add explicit water box
`amber_coordinates` AMBER Coordinates	Input file	AMBER System MD	AMBER coordinate or restart file with positions and, for periodic systems, box vectors. Use a folder, dataset, or previous job source so the topology file is mounted too. Required; Files: .inpcrd, .rst7, .restrt, .crd
`amber_topology` AMBER Topology	Input file	AMBER System MD	Relative path to the matching AMBER topology/parameter file in the same input source. Required; Files: .prmtop, .parm7, .top
`gromacs_coordinates` GROMACS Coordinates	Input file	GROMACS System MD	GROMACS .gro coordinate file with positions and, for periodic systems, box vectors. Upload or select the full folder when the topology includes .itp or force-field files. Required; Files: .gro
`gromacs_topology` GROMACS Topology	Input file	GROMACS System MD	Relative path to the matching .top file in the same input source. Referenced .itp and force-field files must be mounted beside it. Required; Files: .top
`workflow` Workflow	Text	All modes	Run only model cleanup/minimization, or continue into a conventional constant-temperature MD trajectory. Default: Minimize and run dynamics; Options: Minimize and run dynamics, Energy minimize only
`duration_ns` Simulation Time	Number	All modes	Total molecular dynamics time in nanoseconds. Default: 1; Range: 0.001-100; Shown when workflow is Minimize and run dynamics
`temperature_kelvin` Temperature	Number	All modes	Target Langevin thermostat temperature in kelvin. Default: 300; Range: 1-500; Shown when workflow is Minimize and run dynamics
`output_interval_ps` Output Interval	Number	All modes	Time between trajectory/status samples in picoseconds. Default: 10; Range: 0.1-100000; Shown when workflow is Minimize and run dynamics
`trajectory_format` Trajectory Format	Text	All modes	Coordinate trajectory format written during dynamics. Default: DCD trajectory; Options: DCD trajectory, PDB snapshots, Both trajectory formats; Shown when workflow is Minimize and run dynamics

Advanced configuration fields

Parameter	Type	Modes	What it does
`ph` pH	Number	Standard Structure MD	pH used when adding missing hydrogens to standard residues. Default: 7; Range: 0-14
`time_step_fs` Time Step	Number	All modes	Integrator time step in femtoseconds. Defaults to a conservative value for constrained hydrogen bonds. Default: 2; Range: 0.5-4; Shown when workflow is Minimize and run dynamics
`random_seed` Random Seed	Integer	All modes	Use 0 for OpenMM's default random seeding, or set a positive seed for reproducibility. Default: 0; Range: 0-2147483647; Shown when workflow is Minimize and run dynamics

Outputs And Metrics

Prepared, minimized, and final PDB structures.
DCD and/or PDB trajectories when requested.
state.csv with energy, temperature, speed, progress, and timing values.
summary.json plus restart-oriented checkpoint/state files.
Potential energy before/after minimization and after dynamics helps catch setup problems.
Temperature and energy traces in state.csv are basic simulation-health checks.

Common Examples

Fast relaxation: Standard Structure MD, Energy minimize only, dry/nonperiodic for quick geometry cleanup.
Short solvated MD: add explicit water, 1.0 nm padding, 0.15 M salt, 1-5 ns at 300 K.
Prepared ligand complex: AMBER or GROMACS System MD with externally parameterized files.

Example API params

{
  "mode": "structure_md",
  "structure": "model.pdb",
  "workflow": "Energy minimize only",
  "solvent_setup": "Vacuum or dry structure"
}

Caveats

This is not a full production MD protocol with multi-stage equilibration, pressure coupling, restraints, enhanced sampling, or ligand parameterization.
Nonstandard residues, covalent ligands, unusual cofactors, carbohydrates, and modified biomolecules usually need prepared AMBER/GROMACS inputs or a custom script.
Inspect protonation choices manually for serious studies.

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 can run a custom OpenMM script with auxiliary files when the canonical setup is not enough.
Use prepared-system modes for ligands and nonstandard chemistry.

curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer <api_key>" \
  -F program=openmm \
  -F 'params={"mode":"standard_structure_md","structure_file":"model.pdb","workflow":"Energy minimize only","solvent_setup":"Dry/nonperiodic"}'