NAME
g_bond - calculates distances between atoms
VERSION 4.0.1
SYNOPSIS
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
DESCRIPTION
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.
FILES
-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
OTHER OPTIONS
-[no]hno
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]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
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]averyes
Average bond length distributions
-[no]averdistyes
Average distances (turns on -d)
KNOWN PROBLEMS
- It should be possible to get bond information from the topology.
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_bond(1)