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[TRAJECTORY]#

The TRAJECTORY block defines where and how ChemNetworks should retrieve trajectory data. This includes parameters such as the file name, trajectory type, periodic boundary lengths, periodic boundary conditions, etc. This block can be created multiple times to import multiple trajectories into the same ChemNetworks analysis.

NAME#

Usage#

NAME = $trajectory_section_name

Default = trajectory

User defined name of the TRAJECTORY section. Name is required and must be first entry of TRAJECTORY section. Referenced by ADD.NODES.TRAJECTORY to load this trajectory into a graph.

FILE#

Usage#

FILE = $trajectory_file_name [$second_trajectory_file_name]

Default = N/A

Path and name of trajectory file. Requires file extension.

If using TRAJECTORY.TYPE = groxtc, the .gro file should be written first, then the .xtc file.

TYPE#

Usage#

TYPE = < lammpstrj | xyz | gro | xtc | groxtc | dspacestrj >

Default = lammpstrj

Type of trajectory file, identified by extension. We currently support lammpstrj, xyz, gro, xtc, groxtc, and dspacestrj.

For lammpstrj and dspacestrj trajectories, all attributes in the trajectory file will be provided. The x, y, and z attributes must be supplied. If the lammpstrj file uses a different name for the coordinate positions (xs, for example), they will need to be renamed to x, y, or z.

For xyz trajectories, the atom_type, x, y, and z node attributes are provided.

For gro trajectories, the mol_id, mol_type, atom_type, atom_id, x, y, and z node attributes are provided. If velocities are present, then vx, vy, and vz node attributes are also provided. The mol_id and atom_id attributes are typically limited to 99999, as gro files only allow for 5 columns in those attributes. We unroll the looped values for these attributes: 99999 -> 0 -> 1 becomes 99999 -> 100000 -> 100001, etc. This also applies to groxtc trajectories.

For xtc trajectories, the atom_id, x, y, and z node attributes are provided.

For groxtc trajectories, the mol_id, mol_type, atom_type, atom_id, x, y, and z node attributes are provided. Velocities are not provided, even if they're present in the .gro file.

PBC.DIM#

Usage#

PBC.DIM = read | $x_hi $y_hi $z_hi | $x_low $x_hi $y_low $y_hi $z_low $z_hi [$xy $xz $yz]

Default = 0 0 0 0 0 0 0 0 0

Dimensions of the simulation box. Accepts three formats:

  • read reads box dimensions from the trajectory file each frame. Supported by all formats except xyz. Triclinic box geometry (tilt factors) is read automatically when provided in the trajectory.
  • 3 parameters ($x_hi $y_hi $z_hi) sets the box from 0.0 to the given value in each dimension, with zero tilt.
  • 6 or 9 parameters specifies the full low/high bounds in each dimension, optionally with tilt factors.

ChemNetworks applies the minimum image convention for all distance calculations.

SCALE#

Usage#

SCALE = $scalar

Default = 1.0

Scale the coordinates of the trajectory by a non-zero value. This can be useful when the trajectory is written in one unit, but you want to analyze in another. For example, it may be helpful when working with GROMACS files, which are stored in nanometers, but you want to work in angstroms (SCALE = 10), or vice versa.