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

6       g_bond - calculates distances between atoms
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8       VERSION 4.5
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SYNOPSIS

11       g_bond  -f traj.xtc -n index.ndx -s topol.tpr -o bonds.xvg -l bonds.log
12       -d distance.xvg -[no]h -[no]version -nice int -b time -e time -dt  time
13       -[no]w -xvg enum -blen real -tol real -[no]aver -[no]averdist
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DESCRIPTION

16       g_bond  makes a distribution of bond lengths. If all is well a gaussian
17       distribution should be made when using a harmonic potential.  Bonds are
18       read from a single group in the index file in order i1-j1 i2-j2 through
19       in-jn.
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22        -tol gives the half-width of the distribution as  a  fraction  of  the
23       bondlength ( -blen). That means, for a bond of 0.2 a tol of 0.1 gives a
24       distribution from 0.18 to 0.22.
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27       Option  -d plots all  the  distances  as  a  function  of  time.   This
28       requires a structure file for the atom and residue names in the output.
29       If however the option  -averdist is given (as well or  separately)  the
30       average bond length is plotted instead.
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FILES

33       -f traj.xtc Input
34        Trajectory: xtc trr trj gro g96 pdb cpt
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36       -n index.ndx Input
37        Index file
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39       -s topol.tpr Input, Opt.
40        Structure+mass(db): tpr tpb tpa gro g96 pdb
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42       -o bonds.xvg Output
43        xvgr/xmgr file
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45       -l bonds.log Output, Opt.
46        Log file
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48       -d distance.xvg Output, Opt.
49        xvgr/xmgr file
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OTHER OPTIONS

53       -[no]hno
54        Print help info and quit
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56       -[no]versionno
57        Print version info and quit
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59       -nice int 19
60        Set the nicelevel
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62       -b time 0
63        First frame (ps) to read from trajectory
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65       -e time 0
66        Last frame (ps) to read from trajectory
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68       -dt time 0
69        Only use frame when t MOD dt = first time (ps)
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71       -[no]wno
72        View output xvg, xpm, eps and pdb files
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74       -xvg enum xmgrace
75        xvg plot formatting:  xmgrace,  xmgr or  none
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77       -blen real -1
78        Bond length. By default length of first bond
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80       -tol real 0.1
81        Half width of distribution as fraction of blen
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83       -[no]averyes
84        Average bond length distributions
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86       -[no]averdistyes
87        Average distances (turns on -d)
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KNOWN PROBLEMS

91       - It should be possible to get bond information from the topology.
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SEE ALSO

95       gromacs(7)
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97       More   information  about  GROMACS  is  available  at  <http://www.gro‐
98       macs.org/>.
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102                                Thu 26 Aug 2010                      g_bond(1)
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