1GMX-PAIRDIST(1)                     GROMACS                    GMX-PAIRDIST(1)
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NAME

6       gmx-pairdist - Calculate pairwise distances between groups of positions
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SYNOPSIS

9          gmx pairdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                       [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
11                       [-tu <enum>] [-fgroup <selection>] [-xvg <enum>]
12                       [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>]
13                       [-seltype <enum>] [-cutoff <real>] [-type <enum>]
14                       [-refgrouping <enum>] [-selgrouping <enum>]
15                       [-ref <selection>] [-sel <selection>]
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DESCRIPTION

18       gmx pairdist calculates pairwise distances between one reference selec‐
19       tion (given with -ref) and one or more  other  selections  (given  with
20       -sel).   It can calculate either the minimum distance (the default), or
21       the maximum distance (with -type max).   Distances  to  each  selection
22       provided with -sel are computed independently.
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24       By  default,  the global minimum/maximum distance is computed.  To com‐
25       pute more distances (e.g., minimum distances to each residue in  -ref),
26       use  -refgrouping  and/or  -selgrouping  to  specify  how the positions
27       within each selection should be grouped.
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29       Computed distances are written to the file specified with -o.  If there
30       are  N groups in -ref and M groups in the first selection in -sel, then
31       the output contains N*M columns for the first  selection.  The  columns
32       contain distances like this: r1-s1, r2-s1, …, r1-s2, r2-s2, …, where rn
33       is the n’th group in -ref and sn is the n’th group in the other  selec‐
34       tion.  The distances for the second selection comes as separate columns
35       after the first selection, and so on.  If some selections are  dynamic,
36       only  the  selected  positions are used in the computation but the same
37       number of columns is always written out.  If  there  are  no  positions
38       contributing  to some group pair, then the cutoff value is written (see
39       below).
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41       -cutoff sets a cutoff for the computed distances.  If the result  would
42       contain  a distance over the cutoff, the cutoff value is written to the
43       output file instead. By default, no cutoff is used, but if you are  not
44       interested  in  values beyond a cutoff, or if you know that the minimum
45       distance is smaller than a cutoff, you should set this option to  allow
46       the tool to use grid-based searching and be significantly faster.
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48       If  you want to compute distances between fixed pairs, gmx distance may
49       be a more suitable tool.
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OPTIONS

52       Options to specify input files:
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54       -f [<.xtc/.trr/…>] (traj.xtc) (Optional)
55              Input trajectory or single configuration: xtc trr  cpt  gro  g96
56              pdb tng
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58       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
59              Input structure: tpr gro g96 pdb brk ent
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61       -n [<.ndx>] (index.ndx) (Optional)
62              Extra index groups
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64       Options to specify output files:
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66       -o [<.xvg>] (dist.xvg)
67              Distances as function of time
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69       Other options:
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71       -b <time> (0)
72              First frame (ps) to read from trajectory
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74       -e <time> (0)
75              Last frame (ps) to read from trajectory
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77       -dt <time> (0)
78              Only use frame if t MOD dt == first time (ps)
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80       -tu <enum> (ps)
81              Unit for time values: fs, ps, ns, us, ms, s
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83       -fgroup <selection>
84              Atoms  stored in the trajectory file (if not set, assume first N
85              atoms)
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87       -xvg <enum> (xmgrace)
88              Plot formatting: none, xmgrace, xmgr
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90       -[no]rmpbc (yes)
91              Make molecules whole for each frame
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93       -[no]pbc (yes)
94              Use periodic boundary conditions for distance calculation
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96       -sf <file>
97              Provide selections from files
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99       -selrpos <enum> (atom)
100              Selection reference positions: atom, res_com, res_cog,  mol_com,
101              mol_cog,     whole_res_com,     whole_res_cog,    whole_mol_com,
102              whole_mol_cog,   part_res_com,    part_res_cog,    part_mol_com,
103              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
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105       -seltype <enum> (atom)
106              Default  selection  output  positions:  atom,  res_com, res_cog,
107              mol_com, mol_cog, whole_res_com,  whole_res_cog,  whole_mol_com,
108              whole_mol_cog,    part_res_com,    part_res_cog,   part_mol_com,
109              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
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111       -cutoff <real> (0)
112              Maximum distance to consider
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114       -type <enum> (min)
115              Type of distances to calculate: min, max
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117       -refgrouping <enum> (all)
118              Grouping of -ref positions to compute  the  min/max  over:  all,
119              res, mol, none
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121       -selgrouping <enum> (all)
122              Grouping  of  -sel  positions  to compute the min/max over: all,
123              res, mol, none
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125       -ref <selection>
126              Reference positions to calculate distances from
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128       -sel <selection>
129              Positions to calculate distances for
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SEE ALSO

132       gmx(1)
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134       More    information    about    GROMACS    is    available    at     <‐
135       http://www.gromacs.org/>.
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COPYRIGHT

138       2019, GROMACS development team
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1432019.2                           Apr 16, 2019                  GMX-PAIRDIST(1)