.TH g_disre 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_disre - analyzes distance restraints

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_disre\fP
.BI "\-s" " topol.tpr "
.BI "\-f" " traj.xtc "
.BI "\-ds" " drsum.xvg "
.BI "\-da" " draver.xvg "
.BI "\-dn" " drnum.xvg "
.BI "\-dm" " drmax.xvg "
.BI "\-dr" " restr.xvg "
.BI "\-l" " disres.log "
.BI "\-n" " viol.ndx "
.BI "\-q" " viol.pdb "
.BI "\-c" " clust.ndx "
.BI "\-x" " matrix.xpm "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-ntop" " int "
.BI "\-maxdr" " real "
.BI "\-nlevels" " int "
.BI "\-[no]third" ""
.SH DESCRIPTION
\&\fB g_disre\fR computes violations of distance restraints.
\&If necessary, all protons can be added to a protein molecule 
\&using the \fB g_protonate\fR 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 \fB \-q\fR flag is given a \fB .pdb\fR file coloured by the
\&amount of average violations.


\&When the \fB \-c\fR 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.
.SH FILES
.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-ds" " drsum.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-da" " draver.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-dn" " drnum.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-dm" " drmax.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-dr" " restr.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-l" " disres.log" 
.B Output
 Log file 

.BI "\-n" " viol.ndx" 
.B Input, Opt.
 Index file 

.BI "\-q" " viol.pdb" 
.B Output, Opt.
 Protein data bank file 

.BI "\-c" " clust.ndx" 
.B Input, Opt.
 Index file 

.BI "\-x" " matrix.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-ntop"  " int" " 0" 
 Number of large violations that are stored in the log file every step

.BI "\-maxdr"  " real" " 0     " 
 Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data.

.BI "\-nlevels"  " int" " 20" 
 Number of levels in the matrix output

.BI "\-[no]third"  "yes   "
 Use inverse third power averaging or linear for matrix output

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.