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gmx-disre(1)                    GROMACS Manual                    gmx-disre(1)

NAME
       gmx-disre - Analyze distance restraints

SYNOPSIS
       gmx disre [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]]
                 [-ds [<.xvg>]] [-da [<.xvg>]] [-dn [<.xvg>]] [-dm [<.xvg>]]
                 [-dr [<.xvg>]] [-l [<.log>]] [-n [<.ndx>]] [-q [<.pdb>]]
                 [-c [<.ndx>]] [-x [<.xpm>]] [-nice <int>] [-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. If necessary, all
       protons can be added to a protein molecule using the gmx 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.

OPTIONS
       Options to specify input and output files:

       -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
           Run input file: tpr tpb tpa

       -f [<.xtc/.trr/...>] (traj.xtc) (Input)
           Trajectory: xtc trr cpt trj gro g96 pdb tng

       -ds [<.xvg>] (drsum.xvg) (Output)
           xvgr/xmgr file

       -da [<.xvg>] (draver.xvg) (Output)
           xvgr/xmgr file

       -dn [<.xvg>] (drnum.xvg) (Output)
           xvgr/xmgr file

       -dm [<.xvg>] (drmax.xvg) (Output)
           xvgr/xmgr file

       -dr [<.xvg>] (restr.xvg) (Output)
           xvgr/xmgr file

       -l [<.log>] (disres.log) (Output)
           Log file

       -n [<.ndx>] (viol.ndx) (Input, Optional)
           Index file

       -q [<.pdb>] (viol.pdb) (Output, Optional)
           Protein data bank file

       -c [<.ndx>] (clust.ndx) (Input, Optional)
           Index file

       -x [<.xpm>] (matrix.xpm) (Output, Optional)
           X PixMap compatible matrix file

       Other options:

       -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]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
       gromacs(7)

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

VERSION 5.0.6                                                     gmx-disre(1)