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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  out-
       put  from other programs	and/or external	analysis programs to calculate
       more complex things.  For detailed help on the selection	syntax,	please
       use gmx help selections.

       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
       aresname	RA and x < 5a 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  in-
       dependently 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	speci-
       fied, 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.

       To plot coordinates for selections, use gmx trajectory.

OPTIONS
       Options to specify input	files:

       -f [<.xtc/.trr/^a|>] (traj.xtc) (Optional)
	      Input  trajectory	 or  single configuration: xtc trr cpt gro g96
	      pdb tng

       -s [<.tpr/.gro/^a|>] (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: 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

       -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
       2020, GROMACS development team

2020.3				 Jul 09, 2020			 GMX-SELECT(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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