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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Atom Restrain Parameters

SPONGE has a coordinate restrain module that is separate from the CV-side restrain described in collective-variables.md.

This module is initialized directly in the main MD workflow and restrains a list of atoms to reference coordinates.

Input Style

This module currently uses historical flat prefix keys such as restrain_atom_id and restrain_single_weight.

The parser stores grouped TOML keys as prefix_key, so the following TOML form is equivalent and is preferred for new documentation:

[restrain]
atom_id = "restrain_atom_id.txt"
coordinate_in_file = "restrain_ref.txt"
single_weight = 20.0
refcoord_scaling = "com_mol"
calc_virial = true

Minimal Example

[restrain]
atom_id = "restrain_atom_id.txt"
coordinate_in_file = "restrain_ref.txt"
single_weight = 20.0

If neither coordinate_in_file nor amber_rst7 is provided, SPONGE copies the current input coordinates as the restrain reference.

Parameters

Parameter	Scope	Type	Default	Description
atom_id	restrain	string	-	Required atom-list file; enables the module
coordinate_in_file	restrain	string	current input coordinates	Reference coordinate file
amber_rst7	restrain	string	-	Reference coordinates loaded from an AMBER rst7 file
single_weight	restrain	float	20.0	Isotropic restrain weight applied to every restrained atom
weight_in_file	restrain	string	-	Per-atom anisotropic restrain weights; used when single_weight is not set
refcoord_scaling	restrain	string	"no"	How reference coordinates are scaled during box updates
calc_virial	restrain	bool	true	Whether to accumulate restrain virial

refcoord_scaling

Supported values are:

Value	Meaning
"no"	Do not scale the reference
"all"	Scale all reference coordinates with the box
"com_ug"	Scale by unit-group center of mass
"com_res"	Scale by residue center of mass
"com_mol"	Scale by molecule center of mass

Weight Input Modes

Isotropic Weight

[restrain]
atom_id = "restrain_atom_id.txt"
single_weight = 20.0

This applies one scalar force constant to every restrained atom.

Per-atom Anisotropic Weights

[restrain]
atom_id = "restrain_atom_id.txt"
weight_in_file = "restrain_weight.txt"

weight_in_file must contain one wx wy wz triplet per restrained atom.

Notes

• The module is enabled only when restrain_atom_id or atom_id in the restrain scope is present.
• coordinate_in_file takes precedence over amber_rst7.
• If single_weight is not provided, weight_in_file is expected.
• This module is independent of CV restrain; both can be used in the same run if needed.