gromacs/gro format

gromacs/gro format#

Aliases#

gro, gromacs/gro

Implementation: GromacsGroFormat

Overview#

GROMACS .gro structure or trajectory file.

GROMACS is a versatile package for molecular dynamics simulations.

GRO stores atom names, Cartesian coordinates, an optional velocity block, and a periodic box. dpdata reads one or more concatenated frames and can write either a selected frame or the complete trajectory.

Quick examples#

The examples use the preferred alias gromacs/gro; any alias listed above is equivalent.

import dpdata

# Geometry-only data
system = dpdata.System("input_file", fmt="gromacs/gro")

# Write geometry-only data
system.to("gromacs/gro", "output_path")

Conversions#

Convert from this format to System#

dpdata.System(file_name, format_atom_name=True, fmt: Literal['gro'] = None, **kwargs) → dpdata.system.System
dpdata.System(file_name, format_atom_name=True, fmt: Literal['gromacs/gro'] = None, **kwargs) → dpdata.system.System
dpdata.System.from_gro(file_name, format_atom_name=True, **kwargs) → dpdata.system.System
dpdata.System.from_gromacs_gro(file_name, format_atom_name=True, **kwargs) → dpdata.system.System

Load gromacs .gro file.

Parameters:
file_namestr

The input file name

format_atom_namebool

Whether to format the atom name

**kwargsdict

Additional format arguments accepted for API compatibility.

Returns:
System

converted system

Convert from System to this format#

dpdata.System.to(fmt: Literal['gro'], file_name: 'FileType | None' = None, frame_idx=-1, **kwargs)
dpdata.System.to(fmt: Literal['gromacs/gro'], file_name: 'FileType | None' = None, frame_idx=-1, **kwargs)
dpdata.System.to_gro(file_name: 'FileType | None' = None, frame_idx=-1, **kwargs)
dpdata.System.to_gromacs_gro(file_name: 'FileType | None' = None, frame_idx=-1, **kwargs)

Dump the system in gromacs .gro format.

Parameters:
file_namestr or None

The output file name. If None, return the file content as a string

frame_idxint

The index of the frame to dump

**kwargsdict

Additional writer options described below.

Other Parameters:
resnamestr, default=”MOL”

Residue name written for every atom.

shiftint, default=0

Offset added to the one-based atom serial numbers.

Convert from LabeledSystem to this format#

dpdata.LabeledSystem.to(fmt: Literal['gro'], file_name: 'FileType | None' = None, frame_idx=-1, **kwargs)
dpdata.LabeledSystem.to(fmt: Literal['gromacs/gro'], file_name: 'FileType | None' = None, frame_idx=-1, **kwargs)
dpdata.LabeledSystem.to_gro(file_name: 'FileType | None' = None, frame_idx=-1, **kwargs)
dpdata.LabeledSystem.to_gromacs_gro(file_name: 'FileType | None' = None, frame_idx=-1, **kwargs)

Dump the system in gromacs .gro format.

Parameters:
file_namestr or None

The output file name. If None, return the file content as a string

frame_idxint

The index of the frame to dump

**kwargsdict

Additional writer options described below.

Other Parameters:
resnamestr, default=”MOL”

Residue name written for every atom.

shiftint, default=0

Offset added to the one-based atom serial numbers.