Client Image Molecule with MDTraj

Welcome to

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A command-line interface for Molecular Dynamics Analysis routines.

version: 0.11.2

Make molecules whole.

Attempts to “Recenter and apply periodic boundary conditions to the molecules in each frame of the trajectory.” (MDTraj documentation)

Algorithm

Uses MDTraj.Trajectory.image_molecule and MDTraj.Topology.find_molecules.

Protocol 1

Performs mdtraj.top.find_molecules and mdtraj.traj.image_molecules in the trajectory as a whole. anchor_molecules parameters get mdtraj.top.find_molecules[:1], and other_molecules parameter receives mdtraj.top.find_molecules[1:].

Protocol 2

The same as protocol 1 but executes those steps for each frame separately. Frames are concatenated back to a whole trajectory at the end.

Examples

Basic usage, -o saves the first frame in a separate topology file:

taurenmd imagemol top.pdb traj.dcd -d imaged.dcd -o

For trajectories with non-standard molecules you can use a TPR file.

taurenmd imagemol top.tpr traj.xtc -d imaged.xtc

Using protocol 2

taurenmd imagemol top.tpr traj.xtc -d imaged.xtc -i 2

References

• MD data accessed and/or processed using MDTraj

usage: tmdimagemol [-h] [-v] [-i] [-d TRAJ_OUTPUT] [-o [TOP_OUTPUT]]
                   [--protocol PROTOCOL]
                   topology trajectories [trajectories ...]

Positional Arguments

topology

Path to the topology file.

trajectories

Path to the trajectory files. If multiple files are given, trajectories will be concatenated by input order.

Named Arguments

-v, --version

show program’s version number and exit

-i, --insort

Sorts input trajectories paths according to their tail numbers, if paths are formatted as follows: my_trajectory_#.dcd, where # is a number. Defaults to False.

Default: False

-d, --traj-output

Modified trajectory output file name. File type will be defined by file name extension. Defaults to traj_out.dcd.

Default: “traj_out.dcd”

-o, --top-output

Export edited trajectory first frame as topololy file. You can specify the exact file name, otherwise, defaults to input trajectory path + ‘frame0.pdb’. Also, if name starts with ‘’, it is used as file suffix, if name ends with ‘_’, it is used as prefix, instead.

Default: False

--protocol

The protocol with which reimage. Read main command description for details.

Default: 1