List of trajectory converters

ASE

Converts a trajectory to MDT format using ASE.

Attempts to convert a trajectory file to MDANSE .mdt format (HDF5). The conversion is done using the ase.io module. It works both for the ASE’s own .traj format, and for other formats supported by ASE. Please help the ASE format detection mechanism by using standard input file names.

Inputs:

• trajectory_file: ASEFileConfigurator default=INPUT_FILENAME

• atom_aliases: AtomMappingConfigurator default={}

• time_step: FloatConfigurator default=1.0

• time_unit: SingleChoiceConfigurator default=fs

• n_steps: IntegerConfigurator default=0

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

CASTEP

Converts a Castep Trajectory into an MDT trajectory file.

Inputs:

• castep_file: MDFileConfigurator default=INPUT_FILENAME.md

• atom_aliases: AtomMappingConfigurator default={}

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

CHARMM

Converts a CHARMM trajectory to an MDT trajectory.

Inputs:

• pdb_file: InputFileConfigurator default=INPUT_FILENAME.pdb

• dcd_file: InputFileConfigurator default=INPUT_FILENAME.dcd

• time_step: FloatConfigurator default=1.0

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

CP2K

Converts a CP2K trajectory to an MDT trajectory.

Inputs:

• pos_file: XYZFileConfigurator default=INPUT_FILENAME.xyz

• vel_file: OptionalXYZFileConfigurator default=

• force_file: OptionalXYZFileConfigurator default=

• cell_file: InputFileConfigurator default=INPUT_FILENAME.cell

• atom_aliases: AtomMappingConfigurator default={}

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

DCD

Converts a DCD trajectory to an MDT trajectory.

Inputs:

• pdb_file: InputFileConfigurator default=INPUT_FILENAME.pdb

• dcd_file: InputFileConfigurator default=INPUT_FILENAME.dcd

• time_step: FloatConfigurator default=1.0

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

DFTB

Converts a DFTB trajectory to an MDT trajectory.

Inputs:

• xtd_file: XTDFileConfigurator default=INPUT_FILENAME.xtd

• trj_file: InputFileConfigurator default=INPUT_FILENAME.trj

• atom_aliases: AtomMappingConfigurator default={}

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

DL_POLY

Converts a DL_POLY trajectory to an MDT trajectory.

Inputs:

• field_file: FieldFileConfigurator default=INPUT_FILENAME

• history_file: InputFileConfigurator default=INPUT_FILENAME

• atom_aliases: AtomMappingConfigurator default={}

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

Forcite

Converts a Forcite trajectory to an MDT trajectory.

Inputs:

• xtd_file: XTDFileConfigurator default=INPUT_FILENAME.xtd

• trj_file: InputFileConfigurator default=INPUT_FILENAME.trj

• atom_aliases: AtomMappingConfigurator default={}

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

Gromacs

Converts a Gromacs trajectory to an MDT trajectory.

Inputs:

• pdb_file: InputFileConfigurator default=INPUT_FILENAME.pdb

• xtc_file: InputFileConfigurator default=INPUT_FILENAME.xtc

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

LAMMPS

Converts a LAMMPS trajectory to an MDT trajectory.

Inputs:

• config_file: ConfigFileConfigurator default=INPUT_FILENAME.config

• trajectory_file: InputFileConfigurator default=INPUT_FILENAME.lammps

• trajectory_format: SingleChoiceConfigurator default=custom

• lammps_units: SingleChoiceConfigurator default=real

• atom_type: SingleChoiceConfigurator default=From config

• atom_aliases: AtomMappingConfigurator default={}

• time_step: FloatConfigurator default=1.0

• n_steps: IntegerConfigurator default=0

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

MDAnalysis

Converts a trajectory to the MDT format using MDAnalysis.

MDAnalysis reads MD trajectories by specifying topology and coordinate files. Multiple files can be used for the coordinate files so that trajectories will be stitched together. For supported file formats, the continuous option ensures that duplicated time-frames will not be added, see <a href=”https://userguide.mdanalysis.org/stable/reading_and_writing.html”>reading and writing</a>. For topology and coordinate files supported by MDAnalysis see <a href=”https://userguide.mdanalysis.org/stable/formats/index.html#formats”>formats</a>.

Inputs:

• topology_file: MDAnalysisTopologyFileConfigurator default=INPUT_FILENAME

• coordinate_files: MDAnalysisCoordinateFileConfigurator default=

• atom_aliases: AtomMappingConfigurator default={}

• time_step: MDAnalysisTimeStepConfigurator default=0.0

• fold: BooleanConfigurator default=False

• continuous: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

MDTraj

Converts a trajectory to the MDT format using MDTraj.

MDTraj reads MD trajectories by specifying trajectory files and optionally a topology file. Multiple files can be used for the trajectory files so that trajectories will be stitched together.

Inputs:

• coordinate_files: MDTrajTrajectoryFileConfigurator default=[“INPUT_FILENAME”]

• topology_file: MDTrajTopologyFileConfigurator default=

• atom_aliases: AtomMappingConfigurator default={}

• time_step: MDTrajTimeStepConfigurator default=0.0

• fold: BooleanConfigurator default=False

• discard_overlapping_frames: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

NAMD

Converts a NAMD trajectory to an MDT trajectory.

Inputs:

• pdb_file: InputFileConfigurator default=INPUT_FILENAME.pdb

• dcd_file: InputFileConfigurator default=INPUT_FILENAME.dcd

• time_step: FloatConfigurator default=1.0

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

VASP

Converts a VASP XDATCAR file to an MDT trajectory.

This converter works for XDATCAR files which contain a header specifying the unit cell size and atom types.

If your XDATCAR file does not have a header, you can add it manually to the beginning of the file. The header can be copied from the CONTCAR file.

A valid header should look like this:

unknown system
1
9.050041    0.000000    0.000000
0.000000    8.236754    0.000000
0.000000    0.000000   11.000452
Cu   Rb   Cl    S
9   4   7   12

where the last two lines specify the atomic types and the number of the atoms of each type in the same order as they appear in the atom coordinates below.

Inputs:

• xdatcar_file: XDATCARFileConfigurator default=INPUT_FILENAME

• atom_aliases: AtomMappingConfigurator default={}

• time_step: FloatConfigurator default=1.0

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A

XPLOR

Converts an Xplor trajectory to an MDT trajectory.

Inputs:

• pdb_file: InputFileConfigurator default=INPUT_FILENAME.pdb

• dcd_file: InputFileConfigurator default=INPUT_FILENAME.dcd

• time_step: FloatConfigurator default=1.0

• fold: BooleanConfigurator default=False

• output_files: OutputTrajectoryConfigurator default=N/A