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g_bond_d
Langue: en
Version: 251184 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
g_bond - calculates bond length distributionsSYNOPSIS
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]averdistDESCRIPTION
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 InputGeneric 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 noPrint 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/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre