g_bond(1)

NAME

g_bond - calculates bond length distributions

SYNOPSIS

g_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

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 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: 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

OTHER OPTIONS

-[no]h 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 no: View output xvg, xpm, eps and pdb files
-[no]xvgr 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 yes: Average bond length distributions
-[no]averdist yes: Average distances (turns on -d)
- It should be possible to get bond information from the topology.

docs.sk

comprehensive documentation repository

See also