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Core Simulation Parameters

Simulation Identity

Parameter Type Default Description
md_name string "Default SPONGE MD Task Name" Simulation task name

Simulation Mode

Parameter Type Default Description
mode string required Simulation mode

mode options:

Value Description
"nve" Microcanonical ensemble (constant energy)
"nvt" Canonical ensemble (constant temperature), requires thermostat
"npt" Isothermal-isobaric ensemble, requires thermostat + barostat
"minimization" / "min" Energy minimization
"rerun" Trajectory reanalysis

Periodic Boundary Conditions

Parameter Type Default Description
pbc bool true Enable periodic boundary conditions

If pbc = false, SPONGE switches to the no-PBC path. This cannot be used with npt, is not supported in multi-process mode, and expects a very large box.

Time and Steps

Parameter Type Default Description
step_limit int 1000 Total simulation steps
dt float 0.001 Time step (ps)
frame_limit int - Frame limit for rerun mode

Force Cutoff

Parameter Type Default Description
cutoff float 8.0 Non-bonded interaction cutoff distance (A)
skin float 2.0 Neighbor list skin distance (A)

Temperature and Pressure Targets

Parameter Type Default Description
target_temperature float 300.0 Top-level target temperature (K), used in NVT/NPT
target_pressure float 1.0 Top-level target pressure (bar), used in NPT

These two keys stay at the top level even when thermostat and barostat options are written in [thermostat] and [barostat].

Temperature and pressure also support schedules through the top-level keys target_temperature_schedule_* and target_pressure_schedule_*. See Thermostat and Barostat.

Initial Velocities

SPONGE preserves the velocities supplied by the selected input loader unless initialization is requested explicitly:

[initial_velocity]
mode = "maxwell"
seed = 202607220001

mode = "maxwell" samples velocities at the step-zero target temperature, removes center-of-mass motion, projects constrained systems onto the SHAKE/SETTLE velocity manifold without moving their coordinates, and rescales using the final system degrees of freedom. seed is required and must be an integer in 0..INT64_MAX; it is independent of thermostat seeds. This mode is available for dynamical simulations, not minimization or rerun.

Working Directory

Parameter Type Default Description
workspace string directory of mdin file Working directory path, can be absolute or relative