1GMX-MINDIST(1)                      GROMACS                     GMX-MINDIST(1)
2
3
4

NAME

6       gmx-mindist - Calculate the minimum distance between two groups
7

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]
16

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.
26
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.
34
35       Also gmx distance and gmx pairdist calculate distances.
36

OPTIONS

38       Options to specify input files:
39
40       -f [<.xtc/.trr/…>] (traj.xtc)
41              Trajectory: xtc trr cpt gro g96 pdb tng
42
43       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
44              Structure+mass(db): tpr gro g96 pdb brk ent
45
46       -n [<.ndx>] (index.ndx) (Optional)
47              Index file
48
49       Options to specify output files:
50
51       -od [<.xvg>] (mindist.xvg)
52              xvgr/xmgr file
53
54       -on [<.xvg>] (numcont.xvg) (Optional)
55              xvgr/xmgr file
56
57       -o [<.out>] (atm-pair.out) (Optional)
58              Generic output file
59
60       -ox [<.xtc/.trr/…>] (mindist.xtc) (Optional)
61              Trajectory: xtc trr gro g96 pdb tng
62
63       -or [<.xvg>] (mindistres.xvg) (Optional)
64              xvgr/xmgr file
65
66       Other options:
67
68       -b <time> (0)
69              Time of first frame to read from trajectory (default unit ps)
70
71       -e <time> (0)
72              Time of last frame to read from trajectory (default unit ps)
73
74       -dt <time> (0)
75              Only use frame when t MOD dt = first time (default unit ps)
76
77       -tu <enum> (ps)
78              Unit for time values: fs, ps, ns, us, ms, s
79
80       -[no]w (no)
81              View output .xvg, .xpm, .eps and .pdb files
82
83       -xvg <enum> (xmgrace)
84              xvg plot formatting: xmgrace, xmgr, none
85
86       -[no]matrix (no)
87              Calculate half a matrix of group-group distances
88
89       -[no]max (no)
90              Calculate maximum distance instead of minimum
91
92       -d <real> (0.6)
93              Distance for contacts
94
95       -[no]group (no)
96              Count contacts with multiple atoms in the first group as one
97
98       -[no]pi (no)
99              Calculate minimum distance with periodic images
100
101       -[no]split (no)
102              Split graph where time is zero
103
104       -ng <int> (1)
105              Number of secondary groups to  compute  distance  to  a  central
106              group
107
108       -[no]pbc (yes)
109              Take periodic boundary conditions into account
110
111       -[no]respertime (no)
112              When writing per-residue distances, write distance for each time
113              point
114
115       -[no]printresname (no)
116              Write residue names
117

SEE ALSO

119       gmx(1)
120
121       More    information    about    GROMACS    is    available    at     <‐
122       http://www.gromacs.org/>.
123
125       2020, GROMACS development team
126
127
128
129
1302019.6                           Feb 28, 2020                   GMX-MINDIST(1)
Impressum