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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Constraint Algorithm Parameters
Constraint Mode
| Parameter | Type | Default | Description |
|---|
constrain_mode | string | none (constraints disabled) | Constraint algorithm |
constrain_mode options:
| Value | Description |
|---|
"SETTLE" | SETTLE algorithm, specialized for rigid water molecules (triangle constraints) |
"SHAKE" | SHAKE algorithm, general bond length constraints |
The base constraint list is configured through the [constrain] prefix:
constrain_mode = "SHAKE"
[constrain]
mass = 3.3
SETTLE Parameters
| Parameter | Type | Default | Description |
|---|
settle_disable | bool | false | Top-level flag that disables SETTLE entirely |
SHAKE Parameters
| Parameter | Scope | Type | Default | Description |
|---|
iteration_numbers | SHAKE | int | 25 | Maximum SHAKE iteration count |
step_length | SHAKE | float | 1.0 | SHAKE step length / damping factor |
[constrain] Parameters
| Parameter | Scope | Type | Default | Description |
|---|
in_file | constrain | string | - | Extra bond-constraint list file |
mass | constrain | float | 3.3, or 0.0 when in_file is set | Auto-constrain bonds involving atoms lighter than this threshold |
angle | constrain | bool | false | Reserved, currently not implemented |
