1g_disre(1)                GROMACS suite, VERSION 4.5                g_disre(1)
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NAME

6       g_disre - analyzes distance restraints
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8       VERSION 4.5
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SYNOPSIS

11       g_disre  -s  topol.tpr  -f  traj.xtc  -ds  drsum.xvg -da draver.xvg -dn
12       drnum.xvg -dm drmax.xvg -dr restr.xvg  -l  disres.log  -n  viol.ndx  -q
13       viol.pdb  -c  clust.ndx  -x matrix.xpm -[no]h -[no]version -nice int -b
14       time -e time -dt time -[no]w -xvg enum -ntop int -maxdr  real  -nlevels
15       int -[no]third
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DESCRIPTION

18       g_disre  computes  violations of distance restraints.  If necessary all
19       protons can be added to a protein molecule using the protonate program.
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22       The program always computes the instantaneous  violations  rather  than
23       time-averaged,  because  this  analysis  is done from a trajectory file
24       afterwards it does not make sense to use time averaging.  However,  the
25       time averaged values per restraint are given in the log file.
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28       An index file may be used to select specific restraints for printing.
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31       When the optional -q flag is given a pdb file coloured by the amount of
32       average violations.
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35       When the  -c option is given, an index file will be read containing the
36       frames  in  your  trajectory  corresponding to the clusters (defined in
37       another manner) that you want to analyze. For these clusters  the  pro‐
38       gram  will  compute  average violations using the third power averaging
39       algorithm and print them in the log file.
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FILES

42       -s topol.tpr Input
43        Run input file: tpr tpb tpa
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45       -f traj.xtc Input
46        Trajectory: xtc trr trj gro g96 pdb cpt
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48       -ds drsum.xvg Output
49        xvgr/xmgr file
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51       -da draver.xvg Output
52        xvgr/xmgr file
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54       -dn drnum.xvg Output
55        xvgr/xmgr file
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57       -dm drmax.xvg Output
58        xvgr/xmgr file
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60       -dr restr.xvg Output
61        xvgr/xmgr file
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63       -l disres.log Output
64        Log file
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66       -n viol.ndx Input, Opt.
67        Index file
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69       -q viol.pdb Output, Opt.
70        Protein data bank file
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72       -c clust.ndx Input, Opt.
73        Index file
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75       -x matrix.xpm Output, Opt.
76        X PixMap compatible matrix file
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OTHER OPTIONS

80       -[no]hno
81        Print help info and quit
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83       -[no]versionno
84        Print version info and quit
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86       -nice int 19
87        Set the nicelevel
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89       -b time 0
90        First frame (ps) to read from trajectory
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92       -e time 0
93        Last frame (ps) to read from trajectory
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95       -dt time 0
96        Only use frame when t MOD dt = first time (ps)
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98       -[no]wno
99        View output xvg, xpm, eps and pdb files
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101       -xvg enum xmgrace
102        xvg plot formatting:  xmgrace,  xmgr or  none
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104       -ntop int 0
105        Number of large violations that are stored in the log file every step
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107       -maxdr real 0
108        Maximum distance violation in matrix output. If less than or equal  to
109       0 the maximum will be determined by the data.
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111       -nlevels int 20
112        Number of levels in the matrix output
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114       -[no]thirdyes
115        Use inverse third power averaging or linear for matrix output
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SEE ALSO

119       gromacs(7)
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121       More   information  about  GROMACS  is  available  at  <http://www.gro‐
122       macs.org/>.
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126                                Thu 26 Aug 2010                     g_disre(1)