dps genmesh

Pack one or more molecule types onto a three-dimensional simulation-box mesh.

Synopsis and options

usage: dps genmesh [-h] -f FILE [FILE ...] -p FILE [FILE ...] -n NUMBER [NUMBER ...] [-g GAP]
                   [-mesh MESH MESH MESH] [-bt {xy,cubic,anisotropy,anosotropy}] [-mx MINIMUM_X]
                   [-my MINIMUM_Y] [-mz MINIMUM_Z] [-s] [--seed SEED] [-ncm] [-oc FILE] [-op FILE]

Pack one or more molecule types onto a three-dimensional simulation-box mesh.

Input:
  -f FILE [FILE ...], --structure FILE [FILE ...]
                        Input structure files (.pdb), one per molecule type. (required)
  -p FILE [FILE ...], --topology FILE [FILE ...]
                        Input topology files (.itp), in the same order as --structure. (required)

Output:
  -oc FILE, --output-conformation FILE
                        Output packed structure file (.pdb); the extension is added if omitted.
                        (default: system.pdb)
  -op FILE, --output-topology FILE
                        Output system topology file (.top); the extension is added if omitted.
                        (default: system.top)

Parameters:
  -h, --help            Show this help message and exit.
  -n NUMBER [NUMBER ...], --number NUMBER [NUMBER ...]
                        Molecule counts, one integer for each input structure. (required)
  -g GAP, --gap GAP     Minimum gap between neighboring molecules, in nm. (default: 1)
  -mesh MESH MESH MESH, --mesh MESH MESH MESH
                        Mesh dimensions NX NY NZ; if omitted, choose a cubic mesh automatically.
                        (default: None)
  -bt {xy,cubic,anisotropy,anosotropy}, --box-type {xy,cubic,anisotropy,anosotropy}
                        Box geometry; 'anosotropy' remains as a deprecated spelling alias.
                        (default: anisotropy)
  -mx MINIMUM_X, --minimum-x MINIMUM_X
                        Minimum box length along x, in nm; zero selects the smallest fitted
                        length. (default: 0)
  -my MINIMUM_Y, --minimum-y MINIMUM_Y
                        Minimum box length along y, in nm; zero selects the smallest fitted
                        length. (default: 0)
  -mz MINIMUM_Z, --minimum-z MINIMUM_Z
                        Minimum box length along z, in nm; zero selects the smallest fitted
                        length. (default: 0)
  -s, --shuffle         Shuffle molecule types before inserting them on the mesh. (default: False)
  --seed SEED           Random seed used when --shuffle is enabled. (default: 1215)
  -ncm, --non-cubic-molecule
                        Use separate molecular extents along x, y, and z instead of one cubic
                        extent. (default: False)

Examples:
  dps genmesh -f chain.pdb -p chain.itp -n 100 -oc system.pdb -op system.top

Note

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