Skip to content

Configuration Reference

All pipeline settings are declared in a single TOML file. Every section is optional except [system].

GROMACS MDP parameter names use hyphens in .mdp files but underscores in the TOML config (e.g., ref-t → ref_t).

[system]

Field Type Required Description
protein path yes Path to the protein PDB file
ligand path no Path to the ligand SDF file (3-D conformer required)
extra_ff_files list[path] no Extra OpenMM ForceField XML files (e.g., metal parameters)
net_charge int no Formal charge of the ligand (auto-detected when omitted)

[forcefield]

Field Type Default Description
protein_ff str "ff14SB" Protein force field. Options: "ff14SB", "ff19SB", "ff99SB"
ligand_ff str "gaff2" Ligand force field. Options: "gaff", "gaff2"
charge_method str "am1bcc" Partial charge method. Options: "am1bcc", "nagl", "espaloma-am1bcc"

[solvation]

Field Type Default Description
water_model str "tip3p" Water model. Options: "tip3p", "tip4p", "tip5p", "spc", "spce"
box_shape str "truncated_octahedron" Box shape. Options: "truncated_octahedron", "cubic"
padding float null Distance (nm) from solute to box edge. Takes precedence over box_size
box_size float 8.0 Absolute box edge length (nm). Used when padding is not set
ion_concentration float 0.15 Salt concentration (mol/L)
neutralize bool true Add counter-ions to neutralize the system

Either padding or box_size must be provided.

[minimization]

Field Type Default Description
nsteps int 10000 Maximum number of minimization steps
emtol float 10.0 Convergence criterion: max force (kJ mol⁻¹ nm⁻¹)

[equilibration]

Field Type Default Description
simulation_time_ps float 500.0 NVT heating duration (ps), ramping from 0 K to 300 K

[md] — Production MD (GROMACS MDP parameters)

The [md] section accepts any field of [GromacsParams][gbsa_pipeline.change_defaults.GromacsParams]. Field names use underscores; they map to hyphenated GROMACS MDP keys.

Integrator

TOML field MDP key Type Default Description
integrator integrator str "md" Integration algorithm: "md" (leapfrog), "md-vv", "sd", "bd"
dt dt float 0.001 Time step (ps)
nsteps nsteps int 500 Number of MD steps
tinit tinit float 0.0 Start time (ps)

Output control

TOML field MDP key Type Default Description
nstlog nstlog int 500 Steps between log entries
nstenergy nstenergy int 500 Steps between energy writes
nstxout_compressed nstxout-compressed int 500 Steps between compressed trajectory frames

Thermostat

TOML field MDP key Type Default Description
tcoupl tcoupl str "no" Thermostat: "no", "berendsen", "nose-hoover", "v-rescale", "andersen"
tc_grps tc-grps str "System" Temperature coupling group(s)
tau_t tau-t float 0.1 Temperature coupling time constant (ps)
ref_t ref-t float 300.0 Reference temperature (K)
nhchainlength nhchainlength int 10 Nosé-Hoover chain length

Barostat

TOML field MDP key Type Default Description
pcoupl pcoupl str "no" Barostat: "no", "Berendsen", "Parrinello-Rahman", "C-rescale", "MTTK"
pcoupltype pcoupltype str "isotropic" Coupling geometry: "isotropic", "semiisotropic", "anisotropic", "surface-tension"
tau_p tau-p float 2.0 Pressure coupling time constant (ps)
ref_p ref-p float 1.0 Reference pressure (bar)
compressibility compressibility float 4.5e-5 Isothermal compressibility (bar⁻¹)

Electrostatics & VdW

TOML field MDP key Type Default Description
coulombtype coulombtype str "PME" Electrostatics method
rcoulomb rcoulomb float 1.2 Coulomb cutoff (nm)
vdw_type vdw-type str "Cut-off" VdW interaction type
rvdw rvdw float 1.2 VdW cutoff (nm)
rvdw_switch rvdw-switch float 1.0 VdW switch start (nm)

Constraints

TOML field MDP key Type Default Description
constraints constraints str "none" Constraint type: "none", "h-bonds", "all-bonds", "h-angles", "all-angles"
constraint_algorithm constraint-algorithm str "LINCS" Solver: "LINCS" or "SHAKE"
lincs_order lincs-order int 4 LINCS expansion order

Velocity generation

TOML field MDP key Type Default Description
gen_vel gen-vel str "no" Generate initial velocities: "yes" or "no"
gen_temp gen-temp float 300.0 Temperature for velocity generation (K)
gen_seed gen-seed int -1 Random seed (-1 = use system clock)