NAME

       g_disre - analyzes distance restraints

       VERSION 4.6.5

SYNOPSIS

       g_disre  -s topol.tpr -f traj.xtc -ds drsum.xvg -da draver.xvg -dn drnum.xvg -dm drmax.xvg
       -dr restr.xvg -l disres.log -n viol.ndx -q viol.pdb  -c  clust.ndx  -x  matrix.xpm  -[no]h
       -[no]version  -nice  int  -b  time -e time -dt time -[no]w -xvg enum -ntop int -maxdr real
       -nlevels int -[no]third

DESCRIPTION

        g_disre computes violations of distance restraints.  If necessary,  all  protons  can  be
       added to a protein molecule using the  g_protonate program.

       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.

FILES

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -ds drsum.xvg Output
        xvgr/xmgr file

       -da draver.xvg Output
        xvgr/xmgr file

       -dn drnum.xvg Output
        xvgr/xmgr file

       -dm drmax.xvg Output
        xvgr/xmgr file

       -dr restr.xvg Output
        xvgr/xmgr file

       -l disres.log Output
        Log file

       -n viol.ndx Input, Opt.
        Index file

       -q viol.pdb Output, Opt.
        Protein data bank file

       -c clust.ndx Input, Opt.
        Index file

       -x matrix.xpm Output, Opt.
        X PixMap compatible matrix file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 19
        Set the nicelevel

       -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]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  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]thirdyes
        Use inverse third power averaging or linear for matrix output

SEE ALSO

       gromacs(7)

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

                                          Mon 2 Dec 2013                               g_disre(1)