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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 always 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 another manner) that you want to analyze. For these clusters
       the program will compute average violations using the third power averaging algorithm 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
       2023, GROMACS development team

2023.3                                            Oct 19, 2023                                      GMX-DISRE(1)