1GMX-MINDIST(1)                      GROMACS                     GMX-MINDIST(1)
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NAME

6       gmx-mindist - Calculate the minimum distance between two groups
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SYNOPSIS

9          gmx mindist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                      [-od [<.xvg>]] [-on [<.xvg>]] [-o [<.out>]]
11                      [-ox [<.xtc/.trr/...>]] [-or [<.xvg>]] [-b <time>]
12                      [-e <time>] [-dt <time>] [-tu <enum>] [-[no]w]
13                      [-xvg <enum>] [-[no]matrix] [-[no]max] [-d <real>]
14                      [-[no]group] [-[no]pi] [-[no]split] [-ng <int>]
15                      [-[no]pbc] [-[no]respertime] [-[no]printresname]
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DESCRIPTION

18       gmx  mindist  computes  the  distance between one group and a number of
19       other groups. Both the minimum distance (between any pair of atoms from
20       the  respective  groups) and the number of contacts within a given dis‐
21       tance are written to two separate output files.  With the -group option
22       a  contact of an atom in another group with multiple atoms in the first
23       group is counted as one contact instead of as multiple contacts.   With
24       -or,  minimum  distances  to each residue in the first group are deter‐
25       mined and plotted as a function of residue number.
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27       With option -pi the minimum distance of a group to its  periodic  image
28       is plotted. This is useful for checking if a protein has seen its peri‐
29       odic image during a simulation. Only one shift  in  each  direction  is
30       considered, giving a total of 26 shifts. Note that periodicity informa‐
31       tion is required from the file supplied with with -s, either as a  .tpr
32       file or a .pdb file with CRYST1 fields.  It also plots the maximum dis‐
33       tance within the group and the lengths of the three box vectors.
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35       Also gmx distance and gmx pairdist calculate distances.
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OPTIONS

38       Options to specify input files:
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40       -f [<.xtc/.trr/…>] (traj.xtc)
41              Trajectory: xtc trr cpt gro g96 pdb tng
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43       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
44              Structure+mass(db): tpr gro g96 pdb brk ent
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46       -n [<.ndx>] (index.ndx) (Optional)
47              Index file
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49       Options to specify output files:
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51       -od [<.xvg>] (mindist.xvg)
52              xvgr/xmgr file
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54       -on [<.xvg>] (numcont.xvg) (Optional)
55              xvgr/xmgr file
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57       -o [<.out>] (atm-pair.out) (Optional)
58              Generic output file
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60       -ox [<.xtc/.trr/…>] (mindist.xtc) (Optional)
61              Trajectory: xtc trr gro g96 pdb tng
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63       -or [<.xvg>] (mindistres.xvg) (Optional)
64              xvgr/xmgr file
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66       Other options:
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68       -b <time> (0)
69              Time of first frame to read from trajectory (default unit ps)
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71       -e <time> (0)
72              Time of last frame to read from trajectory (default unit ps)
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74       -dt <time> (0)
75              Only use frame when t MOD dt = first time (default unit ps)
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77       -tu <enum> (ps)
78              Unit for time values: fs, ps, ns, us, ms, s
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80       -[no]w (no)
81              View output .xvg, .xpm, .eps and .pdb files
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83       -xvg <enum> (xmgrace)
84              xvg plot formatting: xmgrace, xmgr, none
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86       -[no]matrix (no)
87              Calculate half a matrix of group-group distances
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89       -[no]max (no)
90              Calculate maximum distance instead of minimum
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92       -d <real> (0.6)
93              Distance for contacts
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95       -[no]group (no)
96              Count contacts with multiple atoms in the first group as one
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98       -[no]pi (no)
99              Calculate minimum distance with periodic images
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101       -[no]split (no)
102              Split graph where time is zero
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104       -ng <int> (1)
105              Number of secondary groups to  compute  distance  to  a  central
106              group
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108       -[no]pbc (yes)
109              Take periodic boundary conditions into account
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111       -[no]respertime (no)
112              When writing per-residue distances, write distance for each time
113              point
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115       -[no]printresname (no)
116              Write residue names
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SEE ALSO

119       gmx(1)
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121       More    information    about    GROMACS    is    available    at     <‐
122       http://www.gromacs.org/>.
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125       2019, GROMACS development team
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1302019.2                           Apr 16, 2019                   GMX-MINDIST(1)
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