g_bond_d (1) - Linux Manuals
g_bond_d: calculates distances between atoms
NAMEg_bond - calculates distances between atoms
SYNOPSISg_bond -f traj.xtc -n index.ndx -s topol.tpr -o bonds.xvg -l bonds.log -d distance.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -blen real -tol real -[no]aver -[no]averdist
DESCRIPTIONg_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.
FILES-f traj.xtc Input
-nice int 19
-b time 0
-e time 0
-dt time 0
-blen real -1
-tol real 0.1
KNOWN PROBLEMS- It should be possible to get bond information from the topology.
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