Provided by: gromacs-data_4.6.5-1build1_all bug


       g_bond - calculates distances between atoms

       VERSION 4.6.5


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


         g_bond  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.

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

       Option  -d 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  -averdist is given
       (as well or separately) the average bond length is plotted instead.


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input
        Index file

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

       -o bonds.xvg Output
        xvgr/xmgr file

       -l bonds.log Output, Opt.
        Log file

       -d distance.xvg Output, Opt.
        xvgr/xmgr file


        Print help info and quit

        Print version info and quit

       -nice int 19
        Set the nicelevel

       -b time 0
        First frame (ps) to read from trajectory

       -e time 0
        Last frame (ps) to read from trajectory

       -dt time 0
        Only use frame when t MOD dt = first time (ps)

        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

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

       -tol real 0.1
        Half width of distribution as fraction of  -blen

        Average bond length distributions

        Average distances (turns on  -d)


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



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                                g_bond(1)