gmx-select(1) GROMACS Manual gmx-select(1)NAMEgmx-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
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.
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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-select(1)
