Rechercher une page de manuel
g_mindist_d
Langue: en
Version: 258595 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
g_mindist - calculates the minimum distance between two groupsSYNOPSIS
g_mindist -f traj.xtc -s topol.tpr -n index.ndx -od mindist.xvg -on numcont.xvg -o atm-pair.out -ox mindist.xtc -or mindistres.xvg -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -[no]matrix -[no]max -d real -[no]pi -[no]split -ng intDESCRIPTION
g_mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given distance are written to two separate output files. With -or , minimum distances to each residue in the first group are determined and plotted as a function of reisdue number.With option -pi the minimum distance of a group to its periodic image is plotted. This is useful for checking if a protein has seen its periodic image during a simulation. Only one shift in each direction is considered, giving a total of 26 shifts. It also plots the maximum distance within the group and the lengths of the three box vectors.
Other programs that calculate distances are g_dist
and g_bond
FILES
-f traj.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input, Opt.
Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-n index.ndx Input, Opt.
Index file
-od mindist.xvg Output
xvgr/xmgr file
-on numcont.xvg Output, Opt.
xvgr/xmgr file
-o atm-pair.out Output, Opt.
Generic output file
-ox mindist.xtc Output, Opt.
Generic trajectory: xtc trr trj gro g96 pdb
-or mindistres.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)
-tu enum ps
Time unit: ps , fs , ns , us , ms , s , m or h
-[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
-[no]matrix no
Calculate half a matrix of group-group distances
-[no]max no
Calculate *maximum* distance instead of minimum
-d real 0.6
Distance for contacts
-[no]pi no
Calculate minimum distance with periodic images
-[no]split no
Split graph where time is zero
-ng int 1
Number of secondary groups to compute distance to a central group
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