1 .TH g_bond 1 "Fri 19 Apr 2013" "" "GROMACS suite, VERSION 4.5.7"
3 g_bond - calculates distances between atoms
9 .BI "\-n" " index.ndx "
10 .BI "\-s" " topol.tpr "
11 .BI "\-o" " bonds.xvg "
12 .BI "\-l" " bonds.log "
13 .BI "\-d" " distance.xvg "
15 .BI "\-[no]version" ""
25 .BI "\-[no]averdist" ""
27 \&\fB g_bond\fR makes a distribution of bond lengths. If all is well a
28 \&Gaussian distribution should be made when using a harmonic potential.
29 \&Bonds are read from a single group in the index file in order i1\-j1
30 \&i2\-j2 through in\-jn.
33 \&\fB \-tol\fR gives the half\-width of the distribution as a fraction
34 \&of the bondlength (\fB \-blen\fR). That means, for a bond of 0.2
35 \&a tol of 0.1 gives a distribution from 0.18 to 0.22.
38 \&Option \fB \-d\fR plots all the distances as a function of time.
39 \&This requires a structure file for the atom and residue names in
40 \&the output. If however the option \fB \-averdist\fR is given (as well
41 \&or separately) the average bond length is plotted instead.
45 Trajectory: xtc trr trj gro g96 pdb cpt
47 .BI "\-n" " index.ndx"
51 .BI "\-s" " topol.tpr"
53 Structure+mass(db): tpr tpb tpa gro g96 pdb
55 .BI "\-o" " bonds.xvg"
59 .BI "\-l" " bonds.log"
63 .BI "\-d" " distance.xvg"
69 Print help info and quit
71 .BI "\-[no]version" "no "
72 Print version info and quit
74 .BI "\-nice" " int" " 19"
77 .BI "\-b" " time" " 0 "
78 First frame (ps) to read from trajectory
80 .BI "\-e" " time" " 0 "
81 Last frame (ps) to read from trajectory
83 .BI "\-dt" " time" " 0 "
84 Only use frame when t MOD dt = first time (ps)
87 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
89 .BI "\-xvg" " enum" " xmgrace"
90 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
92 .BI "\-blen" " real" " \-1 "
93 Bond length. By default length of first bond
95 .BI "\-tol" " real" " 0.1 "
96 Half width of distribution as fraction of \fB \-blen\fR
98 .BI "\-[no]aver" "yes "
99 Average bond length distributions
101 .BI "\-[no]averdist" "yes "
102 Average distances (turns on \fB \-d\fR)
105 \- It should be possible to get bond information from the topology.
110 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.