dps exchange

Analyze molecular exchange and phase residence times across a planar slab interface.

Synopsis and options

usage: dps exchange [-h] -s FILE -f FILE [-n FILE] -o PREFIX [-ref REFERENCE_GROUP]
                    [-sel SELECTION_GROUPS [SELECTION_GROUPS ...]] [--axis {x,y,z}]
                    [--center-mode {frame,block,none}] [--bin-width BIN_WIDTH]
                    [--dense-phase-threshold DENSE_PHASE_THRESHOLD]
                    [--interface-threshold INTERFACE_THRESHOLD] [-b START_TIME] [-e END_TIME]
                    [-dt DELTA_TIME] [--blocks BLOCKS] [--no-states]

Analyze molecular exchange and phase residence times across a planar slab interface.

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

Output:
  -o PREFIX, --output-prefix PREFIX
                        Output prefix for .profile.xvg, .events.csv, .residence.csv,
                        .survival.csv, .summary.csv, and optional .states.csv files. (required)

Parameters:
  -h, --help            Show this help message and exit.
  -ref REFERENCE_GROUP, --reference-group REFERENCE_GROUP
                        Index group used to locate and fit the dense slab. (default: None)
  -sel SELECTION_GROUPS [SELECTION_GROUPS ...], --selection-groups SELECTION_GROUPS [SELECTION_GROUPS ...]
                        Index groups whose molecules are tracked; if omitted, use the reference
                        group. (default: None)
  --axis {x,y,z}        Interface-normal axis. (default: z)
  --center-mode {frame,block,none}
                        Slab centering strategy: frame aligns every analyzed frame; block uses one
                        center per contiguous --blocks segment; none expects an already centered
                        slab. (default: frame)
  --bin-width BIN_WIDTH
                        Requested reference density-bin width, in nm; shared with density.
                        (default: 0.05)
  --dense-phase-threshold DENSE_PHASE_THRESHOLD
                        Dense-phase threshold as a fraction of the maximum reference density;
                        shared with the density command. (default: 0.5)
  --interface-threshold INTERFACE_THRESHOLD
                        Normalized dilute-side threshold defining the interface state; 0.1 uses
                        the fitted 10--90% region. Must be between 0 and 0.5. (default: 0.1)
  -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)
  --blocks BLOCKS       Number of fit/statistics blocks and block-centering groups. (default: 5)
  --no-states           Skip the potentially large per-frame .states.csv output file. (default:
                        False)

Examples:
  dps exchange -s run.tpr -f run.xtc -o exchange --axis z

Note

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