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g_bond(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_bond(1) |
NAME¶
g_bond - calculates distances between atomsSYNOPSIS¶
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]averdistDESCRIPTION¶
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.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Index file
Structure+mass(db): tpr tpb tpa gro g96 pdb
xvgr/xmgr file
Log file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Bond length. By default length of first bond
Half width of distribution as fraction of blen
Average bond length distributions
Average distances (turns on -d)
KNOWN PROBLEMS¶
- It should be possible to get bond information from the topology.SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |