Provided by: gromacs-data_2019.3-2_all bug

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

       2019, GROMACS development team