Mdrun

Module

viennaptm.gromacs.mdrun

class Mdrun(deffnm: str, **kwargs)

Bases: GromacsCommand

Wrapper for the GROMACS mdrun execution command.

This class runs a molecular dynamics simulation using a prepared run input file (.tpr) identified by a default filename prefix. All standard GROMACS output files are generated using this prefix.

Parameters:

• deffnm (str) – Default filename prefix for input and output files.

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

build_gromacs_cmd()

Construct the gmx mdrun command invocation.

The command uses the default filename prefix to locate the input .tpr file and generate all simulation output files.

Returns:

Command-line argument list suitable for execution.

Return type:

list[str]

expected_outputs()

Declare the primary output files expected from the simulation.

The output structure file (.gro) is resolved relative to the working directory if one is configured.

Returns:

List containing the generated output structure file path.

Return type:

list[pathlib.Path]

Methods

__init__(deffnm, **kwargs)	Initialize a GROMACS command wrapper.
build_command()	Build the full command invocation.
build_gromacs_cmd()	Construct the gmx mdrun command invocation.
expected_outputs()	Declare the primary output files expected from the simulation.
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.