EditConf

Module

viennaptm.gromacs.editconf

class EditConf(input_gro: Path, output_gro: Path, **kwargs)

Bases: GromacsCommand

Wrapper for the GROMACS editconf command.

This class constructs and executes a gmx editconf command to center a structure, define a cubic simulation box, and apply a fixed distance between the solute and the box edge.

The command is built using the configured GROMACS binary and produces a single output .gro file.

Parameters:

• input_gro (pathlib.Path) – Path to the input GRO structure file.

• output_gro (pathlib.Path) – Path to the output GRO structure file.

• kwargs (dict) – Additional keyword arguments forwarded to GromacsCommand.

build_gromacs_cmd()

Construct the gmx editconf command invocation.

The generated command centers the input structure, places it in a cubic simulation box, and enforces a fixed distance between the solute and the box boundary.

Returns:

Command-line argument list suitable for execution.

Return type:

list[str]

expected_outputs()

Declare the files expected to be generated by this command.

This method is typically used by workflow or execution managers to validate successful command completion.

Returns:

List containing the path to the generated output GRO file.

Return type:

list[pathlib.Path]

Methods

__init__(input_gro, output_gro, **kwargs)	Initialize a GROMACS command wrapper.
build_command()	Build the full command invocation.
build_gromacs_cmd()	Construct the gmx editconf command invocation.
expected_outputs()	Declare the files expected to be generated by this command.
inspect_result(result)	Inspect command output for fatal GROMACS errors.
mpi_prefix()	Construct the MPI command prefix.
post_run_checks()	Verify that expected output files were created.
run()	Execute the GROMACS command.