1 .TH g_mindist 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_mindist - calculates the minimum distance between two groups
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-od" " mindist.xvg "
12 .BI "\-on" " numcont.xvg "
13 .BI "\-o" " atm\-pair.out "
14 .BI "\-ox" " mindist.xtc "
15 .BI "\-or" " mindistres.xvg "
17 .BI "\-[no]version" ""
33 .BI "\-[no]respertime" ""
34 .BI "\-[no]printresname" ""
36 \&g_mindist computes the distance between one group and a number of
37 \&other groups. Both the minimum distance
38 \&(between any pair of atoms from the respective groups)
39 \&and the number of contacts within a given
40 \&distance are written to two separate output files.
41 \&With the \fB \-group\fR option a contact of an atom an other group
42 \&with multiple atoms in the first group is counted as one contact
43 \&instead of as multiple contacts.
44 \&With \fB \-or\fR, minimum distances to each residue in the first
45 \&group are determined and plotted as a function of residue number.
48 \&With option \fB \-pi\fR the minimum distance of a group to its
49 \&periodic image is plotted. This is useful for checking if a protein
50 \&has seen its periodic image during a simulation. Only one shift in
51 \&each direction is considered, giving a total of 26 shifts.
52 \&It also plots the maximum distance within the group and the lengths
53 \&of the three box vectors.
56 \&Other programs that calculate distances are \fB g_dist\fR
61 Trajectory: xtc trr trj gro g96 pdb cpt
63 .BI "\-s" " topol.tpr"
65 Structure+mass(db): tpr tpb tpa gro g96 pdb
67 .BI "\-n" " index.ndx"
71 .BI "\-od" " mindist.xvg"
75 .BI "\-on" " numcont.xvg"
79 .BI "\-o" " atm\-pair.out"
83 .BI "\-ox" " mindist.xtc"
85 Trajectory: xtc trr trj gro g96 pdb
87 .BI "\-or" " mindistres.xvg"
93 Print help info and quit
95 .BI "\-[no]version" "no "
96 Print version info and quit
98 .BI "\-nice" " int" " 19"
101 .BI "\-b" " time" " 0 "
102 First frame (ps) to read from trajectory
104 .BI "\-e" " time" " 0 "
105 Last frame (ps) to read from trajectory
107 .BI "\-dt" " time" " 0 "
108 Only use frame when t MOD dt = first time (ps)
110 .BI "\-tu" " enum" " ps"
111 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR
114 View output xvg, xpm, eps and pdb files
116 .BI "\-xvg" " enum" " xmgrace"
117 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
119 .BI "\-[no]matrix" "no "
120 Calculate half a matrix of group\-group distances
122 .BI "\-[no]max" "no "
123 Calculate *maximum* distance instead of minimum
125 .BI "\-d" " real" " 0.6 "
126 Distance for contacts
128 .BI "\-[no]group" "no "
129 Count contacts with multiple atoms in the first group as one
132 Calculate minimum distance with periodic images
134 .BI "\-[no]split" "no "
135 Split graph where time is zero
137 .BI "\-ng" " int" " 1"
138 Number of secondary groups to compute distance to a central group
140 .BI "\-[no]pbc" "yes "
141 Take periodic boundary conditions into account
143 .BI "\-[no]respertime" "no "
144 When writing per\-residue distances, write distance for each time point
146 .BI "\-[no]printresname" "no "
152 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.