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GMX-DISRE(1)			    GROMACS			  GMX-DISRE(1)

NAME
       gmx-disre - Analyze distance restraints

SYNOPSIS
	  gmx disre [-s	[<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
		    [-c	[<.ndx>]] [-ds [<.xvg>]] [-da [<.xvg>]]	[-dn [<.xvg>]]
		    [-dm [<.xvg>]] [-dr	[<.xvg>]] [-l [<.log>]]	[-q [<.pdb>]]
		    [-x	[<.xpm>]] [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
		    [-xvg <enum>] [-ntop <int>]	[-maxdr	<real>]
		    [-nlevels <int>] [-[no]third]

DESCRIPTION
       gmx  disre computes violations of distance restraints.  The program al-
       ways computes the instantaneous violations rather  than	time-averaged,
       because this analysis is	done from a trajectory file afterwards it does
       not make	sense to use time averaging. However, the time averaged	values
       per restraint are given in the log file.

       An  index file may be used to select specific restraints	by index group
       label for printing.

       When the	optional -q flag is given a .pdb file coloured by  the	amount
       of average violations.

       When  the -c option is given, an	index file will	be read	containing the
       frames in your trajectory corresponding to the clusters (defined	in an-
       other manner) that you want to analyze. For these clusters the  program
       will  compute  average violations using the third power averaging algo-
       rithm and print them in the log file.

OPTIONS
       Options to specify input	files:

       -s [<.tpr>] (topol.tpr)
	      Portable xdr run input file

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

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

       -c [<.ndx>] (clust.ndx) (Optional)
	      Index file

       Options to specify output files:

       -ds [<.xvg>] (drsum.xvg)
	      xvgr/xmgr	file

       -da [<.xvg>] (draver.xvg)
	      xvgr/xmgr	file

       -dn [<.xvg>] (drnum.xvg)
	      xvgr/xmgr	file

       -dm [<.xvg>] (drmax.xvg)
	      xvgr/xmgr	file

       -dr [<.xvg>] (restr.xvg)
	      xvgr/xmgr	file

       -l [<.log>] (disres.log)
	      Log file

       -q [<.pdb>] (viol.pdb) (Optional)
	      Protein data bank	file

       -x [<.xpm>] (matrix.xpm)	(Optional)
	      X	PixMap compatible matrix 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)

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

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

       -ntop <int> (0)
	      Number of	large violations that are stored in the	log file every
	      step

       -maxdr <real> (0)
	      Maximum distance violation in matrix output.  If	less  than  or
	      equal to 0 the maximum will be determined	by the data.

       -nlevels	<int> (20)
	      Number of	levels in the matrix output

       -[no]third (yes)
	      Use inverse third	power averaging	or linear for matrix output

SEE ALSO
       gmx(1)

       More	information    about	GROMACS	   is	 available    at    <-
       http://www.gromacs.org/>.

COPYRIGHT
       2025, GROMACS development team

2025.0				 Feb 10, 2025			  GMX-DISRE(1)

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