g_bond(1)

NAME

g_bond - calculates distances between atoms

VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

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

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 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.

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

-[no]versionno
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)

-[no]wno
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

-[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.