dps rmsd

Calculate PBC-aware RMSD with configurable fitting and output granularity.

Synopsis and options

usage: dps rmsd [-h] -s FILE -f FILE [-n FILE] -o FILE [-sel GROUP [GROUP ...] | --select EXPR]
                [-b START_TIME] [-e END_TIME] [-dt DELTA_TIME] [-ref REFERENCE_TIME]
                [--fit-mode {none,molecule,selection}] [--output-mode {molecule,selection}]
                [--mass-weighted] [--summary-only]

Calculate PBC-aware RMSD with configurable fitting and output granularity.

Input:
  -s FILE, --run-input FILE
                        Input DROPPS run file (.tpr) containing topology and coordinates.
                        (required)
  -f FILE, --input FILE
                        Input trajectory file (.xtc). (required)
  -n FILE, --index FILE
                        Optional index file (.ndx) defining additional atom groups. (default:
                        None)
  -sel GROUP [GROUP ...], --selection-groups GROUP [GROUP ...]
                        Index groups containing selected atoms across any number of molecules;
                        molecules are split automatically. (default: None)
  --select EXPR, --selection-expression EXPR
                        DROPPS selection expression applied across all molecules; repeat the
                        option to analyze more than one region. (default: None)

Output:
  -o FILE, --output FILE
                        Output RMSD time series (.xvg); a matching detailed .csv is also written
                        unless --summary-only is used. (required)
  --output-mode {molecule,selection}
                        RMSD calculation/output granularity: one value per molecule or one pooled
                        value for all atoms in each selection. (default: molecule)

Parameters:
  -h, --help            Show this help message and exit.
  -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)
  -ref REFERENCE_TIME, --reference-time REFERENCE_TIME
                        Reference time in ns; the nearest saved frame is used. By default use the
                        first analyzed frame.
  --fit-mode {none,molecule,selection}
                        Coordinate fitting before RMSD: none preserves physical
                        translation/rotation, molecule fits every molecule independently, and
                        selection applies one fit to all atoms in each selection. (default:
                        molecule)
  --mass-weighted       Use atom masses for centering, fitting, and RMSD. (default: False)
  --summary-only        Skip the detailed CSV and write only the XVG time series. (default: False)

Select a region once across all molecule copies. DROPPS splits it by topology molecule and unwraps each complete molecule. Fitting and RMSD reporting can then operate per molecule or per selection.

Examples:
  dps rmsd -s run.tpr -f run.xtc -o rmsd.xvg --select "(mol PROT) & (resid 20-80)"
  dps rmsd -s run.tpr -f run.xtc -o rmsd-system.xvg -sel 1 --fit-mode selection --output-mode selection

Note

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