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: none, xmgrace, xmgr

       -[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

       2020, GROMACS development team