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GMX-MINDIST(1)			    GROMACS			GMX-MINDIST(1)

NAME
       gmx-mindist - Calculate the minimum distance between two	groups

SYNOPSIS
	  gmx mindist [-f [_.xtc/.trr/..._]] [-s [_.tpr/.gro/..._]] [-n	[_.ndx_]]
		      [-od [_.xvg_]] [-on [_.xvg_]] [-o	[_.out_]]
		      [-ox [_.xtc/.trr/..._]] [-or [_.xvg_]] [-b _time_]
		      [-e _time_] [-dt _time_] [-tu _enum_] [-[no]w]
		      [-xvg _enum_] [-[no]matrix] [-[no]max] [-d _real_]
		      [-[no]group] [-[no]pi] [-[no]split] [-ng _int_]
		      [-[no]pbc] [-[no]respertime] [-[no]printresname]

DESCRIPTION
       gmx  mindist  computes  the  distance between one group and a number of
       other groups. Both the minimum distance (between	any pair of atoms from
       the  respective	groups)	and the	number of contacts within a given dis-
       tance are written to two	separate output	files.	With the -group	option
       a  contact of an	atom in	another	group with multiple atoms in the first
       group is	counted	as one contact instead of as multiple contacts.	  With
       -or,  minimum  distances	 to each residue in the	first group are	deter-
       mined and plotted as a function of residue number.

       With option -pi the minimum distance of a group to its  periodic	 image
       is plotted. This	is useful for checking if a protein has	seen its peri-
       odic image during a simulation. Only one	shift  in  each	 direction  is
       considered, giving a total of 26	shifts.	Note that periodicity informa-
       tion is required	from the file supplied with with -s, either as a  .tpr
       file or a .pdb file with	CRYST1 fields.	It also	plots the maximum dis-
       tance within the	group and the lengths of the three box vectors.

       Also gmx	distance and gmx pairdist calculate distances.

OPTIONS
       Options to specify input	files:

       -f [<.xtc/.trr/^a|>] (traj.xtc)
	      Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/^a|>] (topol.tpr) (Optional)
	      Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
	      Index file

       Options to specify output files:

       -od [<.xvg>] (mindist.xvg)
	      xvgr/xmgr	file

       -on [<.xvg>] (numcont.xvg) (Optional)
	      xvgr/xmgr	file

       -o [<.out>] (atm-pair.out) (Optional)
	      Generic output file

       -ox [<.xtc/.trr/^a|>] (mindist.xtc) (Optional)
	      Trajectory: xtc trr gro g96 pdb tng

       -or [<.xvg>] (mindistres.xvg) (Optional)
	      xvgr/xmgr	file

       Other options:

       -b <time> (0)
	      Time of first frame to read from trajectory (default unit	ps)

       -e <time> (0)
	      Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
	      Only use frame when t MOD	dt = first time	(default unit ps)

       -tu <enum> (ps)
	      Unit for time values: fs,	ps, ns,	us, ms,	s

       -[no]w (no)
	      View output .xvg,	.xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
	      xvg plot formatting: xmgrace, xmgr, none

       -[no]matrix (no)
	      Calculate	half a matrix of group-group distances

       -[no]max	(no)
	      Calculate	maximum	distance instead of minimum

       -d <real> (0.6)
	      Distance for contacts

       -[no]group (no)
	      Count contacts with multiple atoms in the	first group as one

       -[no]pi (no)
	      Calculate	minimum	distance with periodic images

       -[no]split (no)
	      Split graph where	time is	zero

       -ng <int> (1)
	      Number of	secondary groups to  compute  distance	to  a  central
	      group

       -[no]pbc	(yes)
	      Take periodic boundary conditions	into account

       -[no]respertime (no)
	      When writing per-residue distances, write	distance for each time
	      point

       -[no]printresname (no)
	      Write residue names

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-MINDIST(1)

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

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