Client RMSD

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A command-line interface for Molecular Dynamics Analysis routines.

version: 0.11.2

Calculates RMSDs for a selection.

Algorithm

Calculates the RMSD values along a trajectory slice for different selections. If multiple selections are given creates a series data for that selection.

RMSD is calculated using libcalc.mda_rmsd.

Examples

Calculate RMSD of the whole system:

taurenmd rmsd top.pdb traj.dcd -e rmsd.csv

Calculates RMSDs for different selections:

taurenmd rmsd top.pdb traj.dcd -g 'segid A' 'segid B' -e

-x exports the data to a CSV file. You can also plot the data with the -v option:

[...] -x rmsd.csv -v title=my-plot-title xlabel=frames ylabel=RMSDs ...

where [...] is the previous command example.

You can also use tmdrmsd instead of taurenmd rmsd.

References

usage: tmdrmsd [-h] [-v] [-i] [-g SELECTIONS [SELECTIONS ...]] [-r REF_FRAME]
               [-s START] [-e STOP] [-p STEP] [-x [EXPORT]]
               [--plot [PLOT [PLOT ...]]]
               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

-g, --selections

List of atom selections to operate with. Selection rules are as defined by the MD analysis library used by the client interface. For instructions read the main command-line client description. Defaults to None, uses a single selection considering all atoms. Example: -g ‘segid A’ ‘segid B’ ‘name CA’

-r, --ref-frame

The frame in the trajectory that serves as reference to compute against.Defaults to 0.

Default: 0

-s, --start

The starting index for the frame slicing. Frames are 0-indexed, so the first frame is -s 0. The starting index is inclusive. Defaults to None, considers from the beginning.

-e, --stop

The ending index for the frame slicing. Frames are 0-indexed, so the last frame of a 500 frame trajectory is index 499, but because the ending index is exclusive, -e 500 is required. Defaults to None, considers to the end.

-p, --step

The periodicity step value for the frame slicing, -p 10 means every 10 frames. Defaults to None, considers every 1 frame.

-x, --export

Export calculated values to a CSV file. Defaults to ‘results.csv’, alternatively, you can give a specific file name.

Default: False

--plot

Plot results. Additional arguments can be given to configure the plot style. Example: –plot xlabel=frames ylabel=RMSD color=red.Accepted plot arguments are defined by the function used to plot the result. The main description of this client which plotting function is used. Defaults to None, no plot is produced.

Default: False