dps editconf

Resize a PDB simulation box and optionally unwrap coordinates along selected axes.

Synopsis and options

usage: dps editconf [-h] -f FILE -o FILE [-x X_AXIS | -mx MULTIPLY_X_AXIS]
                    [-y Y_AXIS | -my MULTIPLY_Y_AXIS] [-z Z_AXIS | -mz MULTIPLY_Z_AXIS] [-px]
                    [-py] [-pz]

Resize a PDB simulation box and optionally unwrap coordinates along selected axes.

Input:
  -f FILE, --structure FILE
                        Input structure file (.pdb). (required)

Output:
  -o FILE, --output FILE
                        Output structure file (.pdb); the extension is added if omitted.
                        (required)

Parameters:
  -h, --help            Show this help message and exit.
  -x X_AXIS, --x-axis X_AXIS
                        New box length along x, in nm. (default: None)
  -mx MULTIPLY_X_AXIS, --multiply-x-axis MULTIPLY_X_AXIS
                        Multiplier applied to the current x box length. (default: None)
  -y Y_AXIS, --y-axis Y_AXIS
                        New box length along y, in nm. (default: None)
  -my MULTIPLY_Y_AXIS, --multiply-y-axis MULTIPLY_Y_AXIS
                        Multiplier applied to the current y box length. (default: None)
  -z Z_AXIS, --z-axis Z_AXIS
                        New box length along z, in nm. (default: None)
  -mz MULTIPLY_Z_AXIS, --multiply-z-axis MULTIPLY_Z_AXIS
                        Multiplier applied to the current z box length. (default: None)
  -px, --treat-pbc-x    Unwrap coordinates across periodic boundaries along x. (default: False)
  -py, --treat-pbc-y    Unwrap coordinates across periodic boundaries along y. (default: False)
  -pz, --treat-pbc-z    Unwrap coordinates across periodic boundaries along z. (default: False)

Examples:
  dps editconf -f system.pdb -o resized.pdb -mx 2 -my 2 -mz 2

Note

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