g_bond_d

Langue: en

Autres versions - même langue

Version: 251184 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

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.

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.