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GMX-PAIRDIST(1)			    GROMACS		       GMX-PAIRDIST(1)

NAME
       gmx-pairdist - Calculate	pairwise distances between groups of positions

SYNOPSIS
	  gmx pairdist [-f [_.xtc/.trr/..._]] [-s [_.tpr/.gro/..._]] [-n [_.ndx_]]
		       [-o [_.xvg_]] [-b _time_] [-e _time_] [-dt _time_]
		       [-tu _enum_] [-fgroup _selection_] [-xvg	_enum_]
		       [-[no]rmpbc] [-[no]pbc] [-sf _file_] [-selrpos _enum_]
		       [-seltype _enum_] [-cutoff _real_] [-type _enum_]
		       [-refgrouping _enum_] [-selgrouping _enum_]
		       [-ref _selection_] [-sel	_selection_]

DESCRIPTION
       gmx pairdist calculates pairwise	distances between one reference	selec-
       tion (given with	-ref) and one or more  other  selections  (given  with
       -sel).	It can calculate either	the minimum distance (the default), or
       the maximum distance (with -type	max).	Distances  to  each  selection
       provided	with -sel are computed independently.

       By  default,  the global	minimum/maximum	distance is computed.  To com-
       pute more distances (e.g., minimum distances to each residue in	-ref),
       use  -refgrouping  and/or  -selgrouping	to  specify  how the positions
       within each selection should be grouped.

       Computed	distances are written to the file specified with -o.  If there
       are  N groups in	-ref and M groups in the first selection in -sel, then
       the output contains N*M columns for the first  selection.  The  columns
       contain	distances like this: r1-s1, r2-s1, a|, r1-s2, r2-s2, a|, where
       rn is the nath group in -ref and	sn is the nath group in	the other  se-
       lection.	 The distances for the second selection	comes as separate col-
       umns after the first selection, and so on.  If some selections are  dy-
       namic,  only the	selected positions are used in the computation but the
       same number of columns is always	written	out.  If there	are  no	 posi-
       tions contributing to some group	pair, then the cutoff value is written
       (see below).

       -cutoff sets a cutoff for the computed distances.  If the result	 would
       contain	a distance over	the cutoff, the	cutoff value is	written	to the
       output file instead. By default,	no cutoff is used, but if you are  not
       interested  in  values beyond a cutoff, or if you know that the minimum
       distance	is smaller than	a cutoff, you should set this option to	 allow
       the tool	to use grid-based searching and	be significantly faster.

       If  you want to compute distances between fixed pairs, gmx distance may
       be a more suitable tool.

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:

       -o [<.xvg>] (dist.xvg)
	      Distances	as function of time

       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

       -cutoff <real> (0)
	      Maximum distance to consider

       -type <enum> (min)
	      Type of distances	to calculate: min, max

       -refgrouping <enum> (all)
	      Grouping of -ref positions to compute  the  min/max  over:  all,
	      res, mol,	none

       -selgrouping <enum> (all)
	      Grouping	of  -sel  positions  to	compute	the min/max over: all,
	      res, mol,	none

       -ref <selection>
	      Reference	positions to calculate distances from

       -sel <selection>
	      Positions	to calculate distances for

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-PAIRDIST(1)

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

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