| 
 | VERSION 3.3.1 | 
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.
| option | filename | type | description | 
|---|---|---|---|
| -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 | 
| option | type | default | description | 
|---|---|---|---|
| -[no]h | bool | 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 | bool | no | View output xvg, xpm, eps and pdb files | 
| -[no]xvgr | bool | 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 | bool | yes | Average bond length distributions | 
| -[no]averdist | bool | yes | Average distances (turns on -d) |