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       g_bond - calculates distances between atoms

       VERSION 4.0.1


       g_bond  -f traj.xtc -n index.ndx -s topol.tpr -o bonds.xvg -l bonds.log
       -d distance.xvg -[no]h -nice int  -b  time  -e  time  -dt  time  -[no]w
       -[no]xvgr -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 thru

        -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

       -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

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

       -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

                                Thu 16 Oct 2008                      g_bond(1)