dps msd

Calculate the mean-square displacement of a selected atom group.

Synopsis and options

usage: dps msd [-h] -s FILE -f FILE [-n FILE] [-sel SELECTION] [-t {xyz,xy,yz,xz,x,y,z}]
               [-b START_TIME] [-e END_TIME] [-dt DELTA_TIME] -o FILE

Calculate the mean-square displacement of a selected atom group.

Input:
  -s FILE, --run-input FILE
                        Input DROPPS run file (.tpr) containing the system and simulation
                        settings. (required)
  -f FILE, --input FILE
                        Input trajectory file (.xtc). (required)
  -n FILE, --index FILE
                        Optional index file (.ndx) defining additional atom groups. (default:
                        None)

Output:
  -o FILE, --output FILE
                        Output mean-square-displacement time series (.xvg); the extension is added
                        if omitted. (required)

Parameters:
  -h, --help            Show this help message and exit.
  -sel SELECTION, --selection SELECTION
                        Index group whose mean-square displacement is calculated; if omitted,
                        prompt interactively. (default: None)
  -t {xyz,xy,yz,xz,x,y,z}, --msd-type {xyz,xy,yz,xz,x,y,z}
                        Cartesian dimensions included in the MSD. (default: xyz)
  -b START_TIME, --start-time START_TIME
                        First trajectory time to analyze, in ns. (default: None)
  -e END_TIME, --end-time END_TIME
                        Last trajectory time to analyze, in ns. (default: None)
  -dt DELTA_TIME, --delta-time DELTA_TIME
                        Approximate interval between analyzed frames, in ns. (default: None)

Examples:
  dps msd -s run.tpr -f run.xtc -o msd.xvg -t xyz

Note

This page is generated from the DROPPS 1.0 argument parser. Run dps msd -h in the installed environment for the same reference at the command line.