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gmx-select(1)			GROMACS	Manual			 gmx-select(1)

NAME
       gmx-select - Print general information about selections

SYNOPSIS
       gmx select [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
		  [-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>] [-xvg <enum>] [-[no]rmpbc]
		  [-[no]pbc] [-sf <file>] [-selrpos <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  out-
       put  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.	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 frac-
       tion covered by the selection. -norm and	-cfnorm	can be specified inde-
       pendently 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  se-
       lected.	-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.

OPTIONS
       Options to specify input	and output files:

       -f [_.xtc/.trr/..._] (traj.xtc) (Input, Optional)
	   Input trajectory or single configuration: xtc trr cpt trj  gro  g96
       pdb tng

       -s [_.tpr/.tpb/..._] (topol.tpr)	(Input,	Optional)
	   Input structure: tpr	tpb tpa	gro g96	pdb brk	ent

       -n [_.ndx_] (index.ndx) (Input, Optional)
	   Extra index groups

       -os [_.xvg_] (size.xvg) (Output,	Optional)
	   Number of positions in each selection

       -oc [_.xvg_] (cfrac.xvg)	(Output, Optional)
	   Covered fraction for	each selection

       -oi [_.dat_] (index.dat)	(Output, Optional)
	   Indices selected by each selection

       -on [_.ndx_] (index.ndx)	(Output, Optional)
	   Index file from the selection

       -om [_.xvg_] (mask.xvg) (Output,	Optional)
	   Mask	for selected positions

       -of [_.xvg_] (occupancy.xvg) (Output, Optional)
	   Occupied fraction for selected positions

       -ofpdb [_.pdb_] (occupancy.pdb) (Output,	Optional)
	   PDB file with occupied fraction for selected	positions

       -olt [_.xvg_] (lifetime.xvg) (Output, 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

       -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

       -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
       gromacs(7)

       More  information  about	 GROMACS  is  available	 at   <http://www.gro-
       macs.org/>.

VERSION	5.0.6							 gmx-select(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO

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