Main Table of Contents

Wed 13 Nov 2013


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.


-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]h bool no Print help info and quit
-[no]version bool no 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]w bool no 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]third bool yes Use inverse third power averaging or linear for matrix output