.TH g_bond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_bond - calculates distances between atoms

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_bond\fP
.BI "\-f" " traj.xtc "
.BI "\-n" " index.ndx "
.BI "\-s" " topol.tpr "
.BI "\-o" " bonds.xvg "
.BI "\-l" " bonds.log "
.BI "\-d" " distance.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-blen" " real "
.BI "\-tol" " real "
.BI "\-[no]aver" ""
.BI "\-[no]averdist" ""
.SH DESCRIPTION
\&\fB g_bond\fR makes a distribution of bond lengths. If all is well a
\&Gaussian distribution should be made when using a harmonic potential.
\&Bonds are read from a single group in the index file in order i1\-j1
\&i2\-j2 through in\-jn.


\&\fB \-tol\fR gives the half\-width of the distribution as a fraction
\&of the bondlength (\fB \-blen\fR). That means, for a bond of 0.2
\&a tol of 0.1 gives a distribution from 0.18 to 0.22.


\&Option \fB \-d\fR plots all the distances as a function of time.
\&This requires a structure file for the atom and residue names in
\&the output. If however the option \fB \-averdist\fR is given (as well
\&or separately) the average bond length is plotted instead.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " index.ndx" 
.B Input
 Index file 

.BI "\-s" " topol.tpr" 
.B Input, Opt.
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-o" " bonds.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-l" " bonds.log" 
.B Output, Opt.
 Log file 

.BI "\-d" " distance.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-blen"  " real" " \-1    " 
 Bond length. By default length of first bond

.BI "\-tol"  " real" " 0.1   " 
 Half width of distribution as fraction of blen

.BI "\-[no]aver"  "yes   "
 Average bond length distributions

.BI "\-[no]averdist"  "yes   "
 Average distances (turns on \fB \-d\fR)

.SH KNOWN PROBLEMS
\- It should be possible to get bond information from the topology.

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.