1g_mindist(1)              GROMACS suite, VERSION 4.5              g_mindist(1)
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NAME

6       g_mindist - calculates the minimum distance between two groups
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8       VERSION 4.5
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SYNOPSIS

11       g_mindist  -f  traj.xtc  -s  topol.tpr -n index.ndx -od mindist.xvg -on
12       numcont.xvg -o atm-pair.out -ox mindist.xtc -or  mindistres.xvg  -[no]h
13       -[no]version  -nice  int  -b time -e time -dt time -tu enum -[no]w -xvg
14       enum -[no]matrix -[no]max -d real -[no]group -[no]pi -[no]split -ng int
15       -[no]pbc -[no]respertime -[no]printresname
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DESCRIPTION

18       g_mindist computes the distance between one group and a number of other
19       groups. Both the minimum distance (between any pair of atoms  from  the
20       respective  groups)  and the number of contacts within a given distance
21       are written to two separate output files.  With the   -group  option  a
22       contact  of  an  atom  an  other 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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28       With option  -pi the minimum distance of a group to its periodic  image
29       is plotted. This is useful for checking if a protein has seen its peri‐
30       odic image during a simulation. Only one shift  in  each  direction  is
31       considered,  giving  a  total  of 26 shifts.  It also plots the maximum
32       distance within the group and the lengths of the three box vectors.
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35       Other programs that calculate distances are  g_dist and  g_bond.
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FILES

38       -f traj.xtc Input
39        Trajectory: xtc trr trj gro g96 pdb cpt
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41       -s topol.tpr Input, Opt.
42        Structure+mass(db): tpr tpb tpa gro g96 pdb
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44       -n index.ndx Input, Opt.
45        Index file
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47       -od mindist.xvg Output
48        xvgr/xmgr file
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50       -on numcont.xvg Output, Opt.
51        xvgr/xmgr file
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53       -o atm-pair.out Output, Opt.
54        Generic output file
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56       -ox mindist.xtc Output, Opt.
57        Trajectory: xtc trr trj gro g96 pdb
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59       -or mindistres.xvg Output, Opt.
60        xvgr/xmgr file
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OTHER OPTIONS

64       -[no]hno
65        Print help info and quit
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67       -[no]versionno
68        Print version info and quit
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70       -nice int 19
71        Set the nicelevel
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73       -b time 0
74        First frame (ps) to read from trajectory
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76       -e time 0
77        Last frame (ps) to read from trajectory
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79       -dt time 0
80        Only use frame when t MOD dt = first time (ps)
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82       -tu enum ps
83        Time unit:  fs,  ps,  ns,  us,  ms or  s
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85       -[no]wno
86        View output xvg, xpm, eps and pdb files
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88       -xvg enum xmgrace
89        xvg plot formatting:  xmgrace,  xmgr or  none
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91       -[no]matrixno
92        Calculate half a matrix of group-group distances
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94       -[no]maxno
95        Calculate *maximum* distance instead of minimum
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97       -d real 0.6
98        Distance for contacts
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100       -[no]groupno
101        Count contacts with multiple atoms in the first group as one
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103       -[no]pino
104        Calculate minimum distance with periodic images
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106       -[no]splitno
107        Split graph where time is zero
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109       -ng int 1
110        Number of secondary groups to compute distance to a central group
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112       -[no]pbcyes
113        Take periodic boundary conditions into account
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115       -[no]respertimeno
116        When writing per-residue distances, write distance for each time point
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118       -[no]printresnameno
119        Write residue names
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SEE ALSO

123       gromacs(7)
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125       More  information  about  GROMACS  is  available  at   <http://www.gro‐
126       macs.org/>.
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130                                Thu 26 Aug 2010                   g_mindist(1)
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