g_bond(1) - Linux man page
Name
g_bond - calculates distances between atomsVERSION 4.5.4-dev-20110404-bc5695c
Synopsis
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.See Also
gromacs(7)More information about GROMACS is available at <http://www.gromacs.org/>.