g_bond VERSION 3.3_beta_20050823

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 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 Generic trajectory: xtc trr trj gro g96 pdb

-n index.ndx Input Index file

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

-o bonds.xvg Output xvgr/xmgr file

-l bonds.log Output, Opt. Log file

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

-[no]h no 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)

-[no]w no View output xvg, xpm, eps and pdb files

-[no]xvgr yes 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

-[no]aver yes Average bond length distributions

-[no]averdist yes Average distances (turns on -d)

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

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.