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)