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

5.1.2                                           February 03, 2016                                   GMX-DISRE(1)