Atom selection keywords

Selection keywords may be used individually or in combination with each other, and each can be repeated any number of times. Selection is incremental: each keyword adds the corresponding atoms to the selection, so that different sets of atoms can be combined. However, atoms included by multiple keywords are only counted once. Below is an example configuration for an atom group called ``atoms''. Note: this is an unusually varied combination of selection keywords, demonstrating how they can be combined together: most simulations only use one of them.

atoms {

  # add atoms 1 and 3 to this group (note: the first atom in the system is 1)
  atomNumbers {
    1 3
  }

  # add atoms starting from 20 up to and including 50
  atomNumbersRange 20-50

  # add all the atoms with occupancy 2 in the file atoms.pdb
  atomsFile atoms.pdb
  atomsCol O
  atomsColValue 2.0

  # add all the C-alphas within residues 11 to 20 of segments "PR1" and "PR2"
  psfSegID PR1 PR2
  atomNameResidueRange CA 11-20
  atomNameResidueRange CA 11-20

  # add index group (requires a .ndx file to be provided globally)
  indexGroup Water
}

The resulting selection includes atoms 1 and 3, those between 20 and 50, the $\mathrm{C}_{\alpha}$ atoms between residues 11 and 20 of the two segments PR1 and PR2, and those in the index group called ``Water''. The indices of this group are read from the file provided by the global keyword indexFile.

In the current version, the Colvars module does not manipulate VMD atom selections directly: however, these can be converted to atom groups within the Colvars configuration string, using selection keywords such as atomNumbers. The complete list of selection keywords available in VMD is:

• atomNumbers $\langle\,$ List of atom numbers$\,\rangle$
  Context: atom group
  Acceptable values: space-separated list of positive integers
  Description: This option adds to the group all the atoms whose numbers are in the list. The number of the first atom in the system is 1: to convert from a VMD selection, use ``atomselect get serial''.

• indexGroup $\langle\,$ Name of index group to be used (GROMACS format)$\,\rangle$
  Context: atom group
  Acceptable values: string
  Description: If the name of an index file has been provided by indexFile, this option allows to select one index group from that file: the atoms from that index group will be used to define the current group.

• atomsOfGroup $\langle\,$ Name of group defined previously$\,\rangle$
  Context: atom group
  Acceptable values: string
  Description: Refers to a group defined previously using its user-defined name. This adds all atoms of that named group to the current group.

• atomNumbersRange $\langle\,$ Atoms within a number range$\,\rangle$
  Context: atom group
  Acceptable values: $<$ Starting number$>$ -$<$ Ending number$>$
  Description: This option includes in the group all atoms whose numbers are within the range specified. The number of the first atom in the system is 1.

• atomNameResidueRange $\langle\,$ Named atoms within a range of residue numbers$\,\rangle$
  Context: atom group
  Acceptable values: $<$ Atom name$>$ $<$ Starting residue$>$ -$<$ Ending residue$>$
  Description: This option adds to the group all the atoms with the provided name, within residues in the given range.

• psfSegID $\langle\,$ PSF segment identifier$\,\rangle$
  Context: atom group
  Acceptable values: space-separated list of strings (max 4 characters)
  Description: This option sets the PSF segment identifier for atomNameResidueRange. Multiple values may be provided, which correspond to multiple instances of atomNameResidueRange, in order of their occurrence. This option is only necessary if a PSF topology file is used.

• atomsFile $\langle\,$ PDB file name for atom selection$\,\rangle$
  Context: atom group
  Acceptable values: UNIX filename
  Description: This option selects atoms from the PDB file provided and adds them to the group according to numerical flags in the column atomsCol. Note: the sequence of atoms in the PDB file provided must match that in the system's topology.

• atomsCol $\langle\,$ PDB column to use for atom selection flags$\,\rangle$
  Context: atom group
  Acceptable values: O, B, X, Y, or Z
  Description: This option specifies which PDB column in atomsFile is used to determine which atoms are to be included in the group.

• atomsColValue $\langle\,$ Atom selection flag in the PDB column$\,\rangle$
  Context: atom group
  Acceptable values: positive decimal
  Description: If defined, this value in atomsCol identifies atoms in atomsFile that are included in the group. If undefined, all atoms with a non-zero value in atomsCol are included.

• dummyAtom $\langle\,$ Dummy atom position (Å)$\,\rangle$
  Context: atom group
  Acceptable values: (x, y, z) triplet
  Description: Instead of selecting any atom, this option makes the group a virtual particle at a fixed position in space. This is useful e.g. to replace a group's center of geometry with a user-defined position.