dps assembly

Analyze the formation, size, composition, and shape of molecular assemblies.

Synopsis and options

usage: dps assembly [-h] -s FILE -f FILE [-n FILE] [-ref REFERENCE_GROUP]
                    [-sel SELECTION_GROUP [SELECTION_GROUP ...]] [-pbc] [-c CUTOFF] [-t THRESHOLD]
                    [-b START_TIME] [-e END_TIME] [-dt DELTA_TIME] [-cn FILE] [-cs FILE]
                    [-csd FILE] [-mf FILE] [-mfc MOLECULE_FRACTION_CUTOFF] [-rgl FILE] [-asp FILE]
                    [-elp FILE]

Analyze the formation, size, composition, and shape of molecular assemblies.

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:
  -cn FILE, --cluster-number FILE
                        Output cluster-count time series (.xvg); the extension is added if
                        omitted. (default: None)
  -cs FILE, --cluster-size FILE
                        Output largest-cluster size time series (.xvg); the extension is added if
                        omitted. (default: None)
  -csd FILE, --cluster-size-distribution FILE
                        Output per-frame cluster-size distributions (.xvg); the extension is added
                        if omitted. (default: None)
  -mf FILE, --molecule-fraction FILE
                        Output selected-group fractions in large clusters (.xvg); the extension is
                        added if omitted. (default: None)
  -rgl FILE, --radius-gyration-largest FILE
                        Output largest-cluster radius-of-gyration time series (.xvg); the
                        extension is added if omitted. (default: None)
  -asp FILE, --asphericity FILE
                        Output asphericity of large clusters (.xvg); the extension is added if
                        omitted. (default: None)
  -elp FILE, --ellipticity FILE
                        Output ellipticity of large clusters (.xvg); the extension is added if
                        omitted. (default: None)

Parameters:
  -h, --help            Show this help message and exit.
  -ref REFERENCE_GROUP, --reference-group REFERENCE_GROUP
                        Reference index group used to determine clusters; if omitted, prompt
                        interactively. (default: None)
  -sel SELECTION_GROUP [SELECTION_GROUP ...], --selection-group SELECTION_GROUP [SELECTION_GROUP ...]
                        Index groups whose molecular fractions in clusters are reported; if
                        omitted, prompt interactively. (default: None)
  -pbc, --treat-pbc     Apply periodic-boundary distances during cluster detection. (default:
                        False)
  -c CUTOFF, --cutoff CUTOFF
                        Bead-contact cutoff used for cluster detection, in nm. (default: 0.7)
  -t THRESHOLD, --threshold THRESHOLD
                        Minimum number of bead contacts required to connect two chains. (default:
                        5)
  -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)
  -mfc MOLECULE_FRACTION_CUTOFF, --molecule-fraction-cutoff MOLECULE_FRACTION_CUTOFF
                        Minimum cluster size used for molecular-fraction and shape analyses.
                        (default: 10)

Examples:
  dps assembly -s run.tpr -f run.xtc -cn clusters.xvg -cs largest.xvg

Note

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