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       g_disre - analyzes distance restraints

       VERSION 4.0.1


       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 -nice int -b time -e time
       -dt time -[no]w -[no]xvgr -ntop int -maxdr real -nlevels int -[no]third


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


       -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


        Print help 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)

        View output xvg, xpm, eps and pdb files

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

       -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

        Use inverse third power averaging or linear for matrix output



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                     g_disre(1)