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)