1GMX-DISRE(1)                        GROMACS                       GMX-DISRE(1)
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NAME

6       gmx-disre - Analyze distance restraints
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SYNOPSIS

9          gmx disre [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
10                    [-c [<.ndx>]] [-ds [<.xvg>]] [-da [<.xvg>]] [-dn [<.xvg>]]
11                    [-dm [<.xvg>]] [-dr [<.xvg>]] [-l [<.log>]] [-q [<.pdb>]]
12                    [-x [<.xpm>]] [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
13                    [-xvg <enum>] [-ntop <int>] [-maxdr <real>]
14                    [-nlevels <int>] [-[no]third]
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DESCRIPTION

17       gmx  disre  computes  violations  of  distance restraints.  The program
18       always computes the instantaneous violations rather than time-averaged,
19       because this analysis is done from a trajectory file afterwards it does
20       not make sense to use time averaging. However, the time averaged values
21       per restraint are given in the log file.
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23       An index file may be used to select specific restraints for printing.
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25       When  the  optional -q flag is given a .pdb file coloured by the amount
26       of average violations.
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28       When the -c option is given, an index file will be read containing  the
29       frames  in  your  trajectory  corresponding to the clusters (defined in
30       another manner) that you want to analyze. For these clusters  the  pro‐
31       gram  will  compute  average violations using the third power averaging
32       algorithm and print them in the log file.
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OPTIONS

35       Options to specify input files:
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37       -s [<.tpr>] (topol.tpr)
38              Portable xdr run input file
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40       -f [<.xtc/.trr/…>] (traj.xtc)
41              Trajectory: xtc trr cpt gro g96 pdb tng
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43       -n [<.ndx>] (viol.ndx) (Optional)
44              Index file
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46       -c [<.ndx>] (clust.ndx) (Optional)
47              Index file
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49       Options to specify output files:
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51       -ds [<.xvg>] (drsum.xvg)
52              xvgr/xmgr file
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54       -da [<.xvg>] (draver.xvg)
55              xvgr/xmgr file
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57       -dn [<.xvg>] (drnum.xvg)
58              xvgr/xmgr file
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60       -dm [<.xvg>] (drmax.xvg)
61              xvgr/xmgr file
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63       -dr [<.xvg>] (restr.xvg)
64              xvgr/xmgr file
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66       -l [<.log>] (disres.log)
67              Log file
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69       -q [<.pdb>] (viol.pdb) (Optional)
70              Protein data bank file
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72       -x [<.xpm>] (matrix.xpm) (Optional)
73              X PixMap compatible matrix file
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75       Other options:
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77       -b <time> (0)
78              Time of first frame to read from trajectory (default unit ps)
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80       -e <time> (0)
81              Time of last frame to read from trajectory (default unit ps)
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83       -dt <time> (0)
84              Only use frame when t MOD dt = first time (default unit ps)
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86       -[no]w (no)
87              View output .xvg, .xpm, .eps and .pdb files
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89       -xvg <enum> (xmgrace)
90              xvg plot formatting: xmgrace, xmgr, none
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92       -ntop <int> (0)
93              Number of large violations that are stored in the log file every
94              step
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96       -maxdr <real> (0)
97              Maximum  distance  violation  in  matrix output. If less than or
98              equal to 0 the maximum will be determined by the data.
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100       -nlevels <int> (20)
101              Number of levels in the matrix output
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103       -[no]third (yes)
104              Use inverse third power averaging or linear for matrix output
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SEE ALSO

107       gmx(1)
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109       More    information    about    GROMACS    is    available    at     <‐
110       http://www.gromacs.org/>.
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113       2019, GROMACS development team
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1182018.7                           May 29, 2019                     GMX-DISRE(1)
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