1 .TH g_disre 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 g_disre - analyzes distance restraints
5 .B VERSION 4.5.4-dev-20110404-bc5695c
8 .BI "\-s" " topol.tpr "
10 .BI "\-ds" " drsum.xvg "
11 .BI "\-da" " draver.xvg "
12 .BI "\-dn" " drnum.xvg "
13 .BI "\-dm" " drmax.xvg "
14 .BI "\-dr" " restr.xvg "
15 .BI "\-l" " disres.log "
16 .BI "\-n" " viol.ndx "
17 .BI "\-q" " viol.pdb "
18 .BI "\-c" " clust.ndx "
19 .BI "\-x" " matrix.xpm "
21 .BI "\-[no]version" ""
29 .BI "\-maxdr" " real "
30 .BI "\-nlevels" " int "
33 \&\fB g_disre\fR computes violations of distance restraints.
34 \&If necessary, all protons can be added to a protein molecule
35 \&using the \fB g_protonate\fR program.
39 \&computes the instantaneous violations rather than time\-averaged,
40 \&because this analysis is done from a trajectory file afterwards
41 \&it does not make sense to use time averaging. However,
42 \&the time averaged values per restraint are given in the log file.
45 \&An index file may be used to select specific restraints for
49 \&When the optional \fB \-q\fR flag is given a \fB .pdb\fR file coloured by the
50 \&amount of average violations.
53 \&When the \fB \-c\fR option is given, an index file will be read
54 \&containing the frames in your trajectory corresponding to the clusters
55 \&(defined in another manner) that you want to analyze. For these clusters
56 \&the program will compute average violations using the third power
57 \&averaging algorithm and print them in the log file.
59 .BI "\-s" " topol.tpr"
61 Run input file: tpr tpb tpa
65 Trajectory: xtc trr trj gro g96 pdb cpt
67 .BI "\-ds" " drsum.xvg"
71 .BI "\-da" " draver.xvg"
75 .BI "\-dn" " drnum.xvg"
79 .BI "\-dm" " drmax.xvg"
83 .BI "\-dr" " restr.xvg"
87 .BI "\-l" " disres.log"
97 Protein data bank file
99 .BI "\-c" " clust.ndx"
103 .BI "\-x" " matrix.xpm"
105 X PixMap compatible matrix file
109 Print help info and quit
111 .BI "\-[no]version" "no "
112 Print version info and quit
114 .BI "\-nice" " int" " 19"
117 .BI "\-b" " time" " 0 "
118 First frame (ps) to read from trajectory
120 .BI "\-e" " time" " 0 "
121 Last frame (ps) to read from trajectory
123 .BI "\-dt" " time" " 0 "
124 Only use frame when t MOD dt = first time (ps)
127 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
129 .BI "\-xvg" " enum" " xmgrace"
130 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
132 .BI "\-ntop" " int" " 0"
133 Number of large violations that are stored in the log file every step
135 .BI "\-maxdr" " real" " 0 "
136 Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data.
138 .BI "\-nlevels" " int" " 20"
139 Number of levels in the matrix output
141 .BI "\-[no]third" "yes "
142 Use inverse third power averaging or linear for matrix output
147 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.