home | help 
GMX-SELECT(1)			     GROMACS			   GMX-SELECT(1)

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 se-
     lections.

     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 an-
     other.

     With  -oc, the fraction covered by each selection is written out as a func-
     tion of time.

     With -oi, the selected atoms/residues/molecules are written out as a  func-
     tion  of time. In the output, the first column contains the frame time, the
     second contains the number of positions, followed by the atom/residue/mole-
     cule 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:  num-
     ber  (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 intu-
     itive, 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  se-
     lected.

     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 posi-
     tions 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 h5md

     -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: xmgrace, xmgr, none

     -[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
     2026, GROMACS development team

2026.3				  Jun 25, 2026			   GMX-SELECT(1)
home | help