1GMX-DISTANCE(1)                     GROMACS                    GMX-DISTANCE(1)
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NAME

6       gmx-distance - Calculate distances between pairs of positions
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SYNOPSIS

9          gmx distance [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                       [-oav [<.xvg>]] [-oall [<.xvg>]] [-oxyz [<.xvg>]]
11                       [-oh [<.xvg>]] [-oallstat [<.xvg>]] [-b <time>]
12                       [-e <time>] [-dt <time>] [-tu <enum>]
13                       [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc]
14                       [-[no]pbc] [-sf <file>] [-selrpos <enum>]
15                       [-seltype <enum>] [-select <selection>] [-len <real>]
16                       [-tol <real>] [-binw <real>]
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DESCRIPTION

19       gmx distance calculates distances between pairs of positions as a func‐
20       tion of time. Each selection specifies an independent set of  distances
21       to  calculate. Each selection should consist of pairs of positions, and
22       the distances are computed between positions 1-2, 3-4, etc.
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24       -oav writes the average distance as a function of time for each  selec‐
25       tion.  -oall writes all the individual distances.  -oxyz does the same,
26       but the x, y, and z components of the distance are written  instead  of
27       the  norm.  -oh writes a histogram of the distances for each selection.
28       The location of the histogram is set with -len and -tol. Bin  width  is
29       set  with  -binw.  -oallstat writes out the average and standard devia‐
30       tion for each individual distance, calculated over the frames.
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32       Note that gmx distance calculates distances between fixed  pairs  (1-2,
33       3-4,  etc.)  within a single selection.  To calculate distances between
34       two selections, including minimum, maximum, and pairwise distances, use
35       gmx pairdist.
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OPTIONS

38       Options to specify input files:
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40       -f [<.xtc/.trr/…>] (traj.xtc) (Optional)
41              Input  trajectory  or  single configuration: xtc trr cpt gro g96
42              pdb tng
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44       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
45              Input structure: tpr gro g96 pdb brk ent
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47       -n [<.ndx>] (index.ndx) (Optional)
48              Extra index groups
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50       Options to specify output files:
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52       -oav [<.xvg>] (distave.xvg) (Optional)
53              Average distances as function of time
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55       -oall [<.xvg>] (dist.xvg) (Optional)
56              All distances as function of time
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58       -oxyz [<.xvg>] (distxyz.xvg) (Optional)
59              Distance components as function of time
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61       -oh [<.xvg>] (disthist.xvg) (Optional)
62              Histogram of the distances
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64       -oallstat [<.xvg>] (diststat.xvg) (Optional)
65              Statistics for individual distances
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67       Other options:
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69       -b <time> (0)
70              First frame (ps) to read from trajectory
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72       -e <time> (0)
73              Last frame (ps) to read from trajectory
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75       -dt <time> (0)
76              Only use frame if t MOD dt == first time (ps)
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78       -tu <enum> (ps)
79              Unit for time values: fs, ps, ns, us, ms, s
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81       -fgroup <selection>
82              Atoms stored in the trajectory file (if not set, assume first  N
83              atoms)
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85       -xvg <enum> (xmgrace)
86              Plot formatting: none, xmgrace, xmgr
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88       -[no]rmpbc (yes)
89              Make molecules whole for each frame
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91       -[no]pbc (yes)
92              Use periodic boundary conditions for distance calculation
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94       -sf <file>
95              Provide selections from files
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97       -selrpos <enum> (atom)
98              Selection  reference positions: atom, res_com, res_cog, mol_com,
99              mol_cog,    whole_res_com,     whole_res_cog,     whole_mol_com,
100              whole_mol_cog,    part_res_com,    part_res_cog,   part_mol_com,
101              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
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103       -seltype <enum> (atom)
104              Default selection  output  positions:  atom,  res_com,  res_cog,
105              mol_com,  mol_cog,  whole_res_com, whole_res_cog, whole_mol_com,
106              whole_mol_cog,   part_res_com,    part_res_cog,    part_mol_com,
107              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
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109       -select <selection>
110              Position pairs to calculate distances for
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112       -len <real> (0.1)
113              Mean distance for histogramming
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115       -tol <real> (1)
116              Width of full distribution as fraction of -len
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118       -binw <real> (0.001)
119              Bin width for histogramming
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SEE ALSO

122       gmx(1)
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124       More     information    about    GROMACS    is    available    at    <‐
125       http://www.gromacs.org/>.
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128       2019, GROMACS development team
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1332018.7                           May 29, 2019                  GMX-DISTANCE(1)
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