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 al‐
18       ways 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 by index group
24       label for printing.
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26       When the optional -q flag is given a .pdb file coloured by  the  amount
27       of average violations.
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29       When  the -c option is given, an index file will be read containing the
30       frames in your trajectory corresponding to the clusters (defined in an‐
31       other  manner) that you want to analyze. For these clusters the program
32       will compute average violations using the third power  averaging  algo‐
33       rithm and print them in the log file.
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OPTIONS

36       Options to specify input files:
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38       -s [<.tpr>] (topol.tpr)
39              Portable xdr run input file
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41       -f [<.xtc/.trr/...>] (traj.xtc)
42              Trajectory: xtc trr cpt gro g96 pdb tng
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44       -n [<.ndx>] (viol.ndx) (Optional)
45              Index file
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47       -c [<.ndx>] (clust.ndx) (Optional)
48              Index file
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50       Options to specify output files:
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52       -ds [<.xvg>] (drsum.xvg)
53              xvgr/xmgr file
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55       -da [<.xvg>] (draver.xvg)
56              xvgr/xmgr file
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58       -dn [<.xvg>] (drnum.xvg)
59              xvgr/xmgr file
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61       -dm [<.xvg>] (drmax.xvg)
62              xvgr/xmgr file
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64       -dr [<.xvg>] (restr.xvg)
65              xvgr/xmgr file
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67       -l [<.log>] (disres.log)
68              Log file
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70       -q [<.pdb>] (viol.pdb) (Optional)
71              Protein data bank file
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73       -x [<.xpm>] (matrix.xpm) (Optional)
74              X PixMap compatible matrix file
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76       Other options:
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78       -b <time> (0)
79              Time of first frame to read from trajectory (default unit ps)
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81       -e <time> (0)
82              Time of last frame to read from trajectory (default unit ps)
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84       -dt <time> (0)
85              Only use frame when t MOD dt = first time (default unit ps)
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87       -[no]w (no)
88              View output .xvg, .xpm, .eps and .pdb files
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90       -xvg <enum> (xmgrace)
91              xvg plot formatting: xmgrace, xmgr, none
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93       -ntop <int> (0)
94              Number of large violations that are stored in the log file every
95              step
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97       -maxdr <real> (0)
98              Maximum distance violation in matrix output.  If  less  than  or
99              equal to 0 the maximum will be determined by the data.
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101       -nlevels <int> (20)
102              Number of levels in the matrix output
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104       -[no]third (yes)
105              Use inverse third power averaging or linear for matrix output
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SEE ALSO

108       gmx(1)
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110       More     information    about    GROMACS    is    available    at    <‐
111       http://www.gromacs.org/>.
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114       2022, GROMACS development team
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1192022.3                           Sep 02, 2022                     GMX-DISRE(1)
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