dps odist

Calculate distances between corresponding beads in two chain groups.

Synopsis and options

usage: dps odist [-h] -s FILE -f FILE [-n FILE] [-ref REFERENCE] [-sel SELECTION] [-b START_TIME]
                 [-e END_TIME] [-dt DELTA_TIME] [-pbc] [-oa FILE] [-ov FILE]

Calculate distances between corresponding beads in two chain groups.

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:
  -oa FILE, --output-average FILE
                        Output chain-averaged distance time series (.xvg); the extension is added
                        if omitted. (default: None)
  -ov FILE, --output-verbose FILE
                        Output all pair distances as a function of time (.xvg); the extension is
                        added if omitted. (default: None)

Parameters:
  -h, --help            Show this help message and exit.
  -ref REFERENCE, --reference REFERENCE
                        Reference index group containing one bead per chain; if omitted, prompt
                        interactively. (default: None)
  -sel SELECTION, --selection SELECTION
                        Selection index group containing one bead per chain; if omitted, prompt
                        interactively. (default: None)
  -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)
  -pbc, --treat-pbc     Unwrap molecules across periodic boundaries before analysis. (default:
                        False)

Examples:
  dps odist -s run.tpr -f run.xtc -oa interchain-distances.xvg

Note

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