NAME

       g_select - selects groups of atoms based on flexible textual selections

       VERSION 4.6.5

SYNOPSIS

       g_select -f traj.xtc -s topol.tpr -sf selection.dat -n index.ndx -os size.xvg -oc cfrac.xvg -oi index.dat
       -om mask.dat -on index.ndx -[no]h -[no]version -nice int -b time -e time -dt time  -xvg  enum  -[no]rmpbc
       -[no]pbc -select string -selrpos enum -seltype enum -[no]dump -[no]norm -[no]cfnorm -resnr enum

DESCRIPTION

         g_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.  Any combination of the output options is possible, but note that  -om only operates
       on the first selection.   -os is the default output option if none is selected.

       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  -dump, the frame time and the
       number of positions is omitted from the output. In this case, only one selection can be given.

       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
       -dump, the frame time is omitted from the output.

FILES

       -f traj.xtc Input, Opt.
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input, Opt.
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -sf selection.dat Input, Opt.
        Generic data file

       -n index.ndx Input, Opt.
        Index file

       -os size.xvg Output, Opt.
        xvgr/xmgr file

       -oc cfrac.xvg Output, Opt.
        xvgr/xmgr file

       -oi index.dat Output, Opt.
        Generic data file

       -om mask.dat Output, Opt.
        Generic data file

       -on index.ndx Output, Opt.
        Index file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 19
        Set the nicelevel

       -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 when t MOD dt = first time (ps)

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -[no]rmpbcyes
        Make molecules whole for each frame

       -[no]pbcyes
        Use periodic boundary conditions for distance calculation

       -select string
        Selection string (use 'help' for help). Note that the whole selection string will need to be  quoted  so
       that  your  shell will pass it in as a string. Example:  g_select -select '"Nearby water" resname SOL and
       within 0.25 of group Protein'

       -selrpos enum atom
        Selection  reference  position:   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 or  dyn_mol_cog

       -seltype enum atom
        Default  analysis  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 or  dyn_mol_cog

       -[no]dumpno
        Do not print the frame time (-om, -oi) or the index size (-oi)

       -[no]normno
        Normalize by total number of positions with -os

       -[no]cfnormno
        Normalize by covered fraction with -os

       -resnr enum number
        Residue number output type:  number or  index

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                      g_select(1)