dps gyrate

Calculate chain radii of gyration and optional distributions.

Synopsis and options

usage: dps gyrate [-h] -s FILE -f FILE [-n FILE]
                  [-sel SELECTION_CALCULATE [SELECTION_CALCULATE ...]] [-b START_TIME]
                  [-e END_TIME] [-dt DELTA_TIME] [-pbc] [-ov FILE] [-oa FILE] [-oh FILE]
                  [-bw BIN_WIDTH]

Calculate chain radii of gyration and optional distributions.

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:
  -ov FILE, --output-verbose FILE
                        Output per-chain radius-of-gyration time series (.xvg); the extension is
                        added if omitted. (default: None)
  -oa FILE, --output-average FILE
                        Output group-averaged radius-of-gyration time series (.xvg); the extension
                        is added if omitted. (default: None)
  -oh FILE, --output-histogram FILE
                        Output radius-of-gyration distribution (.xvg); the extension is added if
                        omitted. (default: None)

Parameters:
  -h, --help            Show this help message and exit.
  -sel SELECTION_CALCULATE [SELECTION_CALCULATE ...], --selection-calculate SELECTION_CALCULATE [SELECTION_CALCULATE ...]
                        Index groups whose chain radii of gyration are calculated; 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)
  -bw BIN_WIDTH, --bin-width BIN_WIDTH
                        Histogram bin width, in nm. (default: 0.1)

At least one output option (-ov, -oa, or -oh) is required.

Examples:
  dps gyrate -s run.tpr -f run.xtc -oa rg-average.xvg

Note

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