-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.
-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
-[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)
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