1GMX-RMSDIST(1)                      GROMACS                     GMX-RMSDIST(1)
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NAME

6       gmx-rmsdist  - Calculate atom pair distances averaged with power -2, -3
7       or -6
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SYNOPSIS

10          gmx rmsdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
11                      [-equiv [<.dat>]] [-o [<.xvg>]] [-rms [<.xpm>]]
12                      [-scl [<.xpm>]] [-mean [<.xpm>]] [-nmr3 [<.xpm>]]
13                      [-nmr6 [<.xpm>]] [-noe [<.dat>]] [-b <time>] [-e <time>]
14                      [-dt <time>] [-[no]w] [-xvg <enum>] [-nlevels <int>]
15                      [-max <real>] [-[no]sumh] [-[no]pbc]
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DESCRIPTION

18       gmx rmsdist computes the root mean square deviation of atom  distances,
19       which  has the advantage that no fit is needed like in standard RMS de‐
20       viation as computed by gmx rms.  The reference structure is taken  from
21       the structure file.  The RMSD at time t is calculated as the RMS of the
22       differences in distance between atom-pairs in the  reference  structure
23       and the structure at time t.
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25       gmx  rmsdist  can  also produce matrices of the rms distances, rms dis‐
26       tances scaled with the mean distance and the mean distances and  matri‐
27       ces  with  NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally,
28       lists of atom pairs with 1/r^3 and 1/r^6 averaged  distance  below  the
29       maximum  distance (-max, which will default to 0.6 in this case) can be
30       generated, by default averaging over equivalent hydrogens (all triplets
31       of hydrogens named *[123]). Additionally a list of equivalent atoms can
32       be supplied (-equiv), each line containing a set  of  equivalent  atoms
33       specified as residue number and name and atom name; e.g.:
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35       HB* 3 SER  HB1 3 SER  HB2
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37       Residue  and atom names must exactly match those in the structure file,
38       including case. Specifying non-sequential atoms is undefined.
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OPTIONS

41       Options to specify input files:
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43       -f [<.xtc/.trr/...>] (traj.xtc)
44              Trajectory: xtc trr cpt gro g96 pdb tng
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46       -s [<.tpr/.gro/...>] (topol.tpr)
47              Structure+mass(db): tpr gro g96 pdb brk ent
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49       -n [<.ndx>] (index.ndx) (Optional)
50              Index file
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52       -equiv [<.dat>] (equiv.dat) (Optional)
53              Generic data file
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55       Options to specify output files:
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57       -o [<.xvg>] (distrmsd.xvg)
58              xvgr/xmgr file
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60       -rms [<.xpm>] (rmsdist.xpm) (Optional)
61              X PixMap compatible matrix file
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63       -scl [<.xpm>] (rmsscale.xpm) (Optional)
64              X PixMap compatible matrix file
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66       -mean [<.xpm>] (rmsmean.xpm) (Optional)
67              X PixMap compatible matrix file
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69       -nmr3 [<.xpm>] (nmr3.xpm) (Optional)
70              X PixMap compatible matrix file
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72       -nmr6 [<.xpm>] (nmr6.xpm) (Optional)
73              X PixMap compatible matrix file
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75       -noe [<.dat>] (noe.dat) (Optional)
76              Generic data file
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78       Other options:
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80       -b <time> (0)
81              Time of first frame to read from trajectory (default unit ps)
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83       -e <time> (0)
84              Time of last frame to read from trajectory (default unit ps)
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86       -dt <time> (0)
87              Only use frame when t MOD dt = first time (default unit ps)
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89       -[no]w (no)
90              View output .xvg, .xpm, .eps and .pdb files
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92       -xvg <enum> (xmgrace)
93              xvg plot formatting: xmgrace, xmgr, none
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95       -nlevels <int> (40)
96              Discretize RMS in this number of levels
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98       -max <real> (-1)
99              Maximum level in matrices
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101       -[no]sumh (yes)
102              Average distance over equivalent hydrogens
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104       -[no]pbc (yes)
105              Use periodic boundary conditions when computing distances
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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-RMSDIST(1)
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