g_select(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_select(1)

NAME

       g_select - selects groups of atoms based on flexible textual selections

       VERSION 4.5.4-dev-20110404-bc5695c

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 out-
       put from other programs and/or external analysis programs to calculate more complex things.  Any combination of the output options is  pos-
       sible, but note that  -om only operates on the first selection.

       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 speci-
       fied 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)

       -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 4 Apr 2011						       g_select(1)