NAME

       gmx-select - Print general information about selections

SYNOPSIS

          gmx select [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                     [-os [<.xvg>]] [-oc [<.xvg>]] [-oi [<.dat>]]
                     [-on [<.ndx>]] [-om [<.xvg>]] [-of [<.xvg>]]
                     [-ofpdb [<.pdb>]] [-olt [<.xvg>]] [-b <time>] [-e <time>]
                     [-dt <time>] [-tu <enum>] [-fgroup <selection>]
                     [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
                     [-selrpos <enum>] [-seltype <enum>] [-select <selection>]
                     [-[no]norm] [-[no]cfnorm] [-resnr <enum>]
                     [-pdbatoms <enum>] [-[no]cumlt]

DESCRIPTION

       gmx  select  writes out basic data about dynamic selections.  It can be used for some simple analyses, or
       the output can be combined with output from other programs and/or external analysis programs to calculate
       more complex things.  For detailed help on the selection syntax, please use gmx help selections.

       Any combination of the output options is  possible,  but  note  that  -om  only  operates  on  the  first
       selection.  Also note that if you provide no output options, no output is produced.

       With  -os, calculates the number of positions in each selection for each frame. With -norm, the output is
       between 0 and 1 and describes the fraction from the maximum number  of  positions  (e.g.,  for  selection
       'resname  RA  and  x  <  5'  the maximum number of positions is the number of atoms in RA residues). With
       -cfnorm, the output is divided by the fraction covered by  the  selection.   -norm  and  -cfnorm  can  be
       specified independently of one another.

       With -oc, the fraction covered by each selection is written out as a function of time.

       With -oi, the selected atoms/residues/molecules are written out as a function of time. In the output, the
       first  column  contains  the  frame  time,  the  second contains the number of positions, followed by the
       atom/residue/molecule numbers.  If more than one selection is specified, the size  of  the  second  group
       immediately follows the last number of the first group and so on.

       With  -on,  the  selected  atoms  are  written as a index file compatible with make_ndx and the analyzing
       tools. Each selection is written as a selection group and for dynamic selections a group is  written  for
       each frame.

       For residue numbers, the output of -oi can be controlled with -resnr: number (default) prints the residue
       numbers  as  they appear in the input file, while index prints unique numbers assigned to the residues in
       the order they appear in the input file, starting with 1. The former is more intuitive, but if the  input
       contains multiple residues with the same number, the output can be less useful.

       With  -om,  a  mask  is  printed  for  the first selection as a function of time. Each line in the output
       corresponds to one frame, and contains either 0/1 for each  atom/residue/molecule  possibly  selected.  1
       stands for the atom/residue/molecule being selected for the current frame, 0 for not selected.

       With  -of,  the  occupancy  fraction of each position (i.e., the fraction of frames where the position is
       selected) is printed.

       With -ofpdb, a PDB file is written out where the occupancy column is filled with the  occupancy  fraction
       of  each  atom  in  the selection. The coordinates in the PDB file will be those from the input topology.
       -pdbatoms can be used to control which atoms appear in the output  PDB  file:  with  all  all  atoms  are
       present,  with  maxsel  all  atoms possibly selected by the selection are present, and with selected only
       atoms that are selected at least in one frame are present.

       With -olt, a histogram is produced that shows the number of selected positions as a function of the  time
       the  position  was  continuously  selected.  -cumlt can be used to control whether subintervals of longer
       intervals are included in the histogram.

       -om, -of, and -olt only make sense with dynamic selections.

       To plot coordinates for selections, use gmx trajectory.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
              Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
              Input structure: tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Extra index groups

       Options to specify output files:

       -os [<.xvg>] (size.xvg) (Optional)
              Number of positions in each selection

       -oc [<.xvg>] (cfrac.xvg) (Optional)
              Covered fraction for each selection

       -oi [<.dat>] (index.dat) (Optional)
              Indices selected by each selection

       -on [<.ndx>] (index.ndx) (Optional)
              Index file from the selection

       -om [<.xvg>] (mask.xvg) (Optional)
              Mask for selected positions

       -of [<.xvg>] (occupancy.xvg) (Optional)
              Occupied fraction for selected positions

       -ofpdb [<.pdb>] (occupancy.pdb) (Optional)
              PDB file with occupied fraction for selected positions

       -olt [<.xvg>] (lifetime.xvg) (Optional)
              Lifetime histogram

       Other options:

       -b <time> (0)
              First frame (ps) to read from trajectory

       -e <time> (0)
              Last frame (ps) to read from trajectory

       -dt <time> (0)
              Only use frame if t MOD dt == first time (ps)

       -tu <enum> (ps)
              Unit for time values: fs, ps, ns, us, ms, s

       -fgroup <selection>
              Atoms stored in the trajectory file (if not set, assume first N atoms)

       -xvg <enum> (xmgrace)
              Plot formatting: xmgrace, xmgr, none

       -[no]rmpbc (yes)
              Make molecules whole for each frame

       -[no]pbc (yes)
              Use periodic boundary conditions for distance calculation

       -sf <file>
              Provide selections from files

       -selrpos <enum> (atom)
              Selection  reference  positions:  atom,  res_com,  res_cog,   mol_com,   mol_cog,   whole_res_com,
              whole_res_cog,    whole_mol_com,    whole_mol_cog,   part_res_com,   part_res_cog,   part_mol_com,
              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

       -seltype <enum> (atom)
              Default selection output positions:  atom,  res_com,  res_cog,  mol_com,  mol_cog,  whole_res_com,
              whole_res_cog,    whole_mol_com,    whole_mol_cog,   part_res_com,   part_res_cog,   part_mol_com,
              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

       -select <selection>
              Selections to analyze

       -[no]norm (no)
              Normalize by total number of positions with -os

       -[no]cfnorm (no)
              Normalize by covered fraction with -os

       -resnr <enum> (number)
              Residue number output type with -oi and -on: number, index

       -pdbatoms <enum> (all)
              Atoms to write with -ofpdb: all, maxsel, selected

       -[no]cumlt (yes)
              Cumulate subintervals of longer intervals in -olt

SEE ALSO

       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2023, GROMACS development team

2023.3                                            Oct 19, 2023                                     GMX-SELECT(1)