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 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)
              First frame (ps) to read from trajectory

       -e <time> (0)
              Last frame (ps) to read from trajectory

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

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

       -xvg <enum>
              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

       2015, GROMACS development team