Organized by GPT-6-Astra. SPONGE 2.0 is under active, iterative development; features, parameters, and documentation may change. Consult the GitHub repository’s docs and skills for the latest version information.
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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 |
